Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T56871 | Target Info | |||
| Target Name | Lysine-specific demethylase 5B (KDM5B) | ||||
| Synonyms | Retinoblastomabinding protein 2 homolog 1; Retinoblastoma-binding protein 2 homolog 1; RBP2H1; RBP2-H1; RBBP2H1; PLU1; PLU-1; Lysinespecific demethylase 5B; Jumonji/ARID domaincontaining protein 1B; Jumonji/ARID domain-containing protein 1B; JARID1B; Histone demethylase JARID1B; Cancer/testis antigen 31; CT31 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | KDM5B | ||||
| Biochemical Class | Paired donor oxygen oxidoreductase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Pyruvic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with pyruvate | PDB:5FY9 | ||||
| Method | X-ray diffraction | Resolution | 2.03 Å | Mutation | No | [1] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKLGG371 GGARDYTLRT381 FGEMADAFKS391 DYFNMPVHMV 401 PTELVEKEFW411 RLVSTIEEDV421 TVEYGADIAS431 KEFGSGFPVR441 DIKLSPEEEE 453 YLDSGWNLNN463 MPVMEQSVLA473 HITADICGMK483 LPWLYVGMCF493 SSFCWHIEDH 503 WSYSINYLHW513 GEPKTWYGVP523 GYAAEQLENV533 MKKLAPELFV543 SQPDLLHQLV 553 TIMNPNTLMT563 HEVPVYRTNQ573 CAGEFVITFP583 RAYHSGFNQG593 FNFAEAVNFC 603 TVDWLPLGRQ613 CVEHYRLLHR623 YCVFSHDEMI633 CKMASKADVL643 DVVVASTVQK 653 DMAIMIEDEK663 ALRETVRKLG673 VIDSERMDFE683 LLPDDERQCV693 KCKTTCFMSA 703 ISCSCKPGLL713 VCLHHVKELC723 SCPPYKYKLR733 YRYTLDDLYP743 MMNALKLRAE 753
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| Ligand Name: Fumaric acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with succinate | PDB:5FY4 | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [2] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: KDOAM25 | Ligand Info | |||||
| Structure Description | Crystal structure of human PLU-1 (JARID1B) in complex with KDOAM25a | PDB:5A3N | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [3] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGKIKL447 SPEEEEYLDS 457 GWNLNNMPVM467 EQSVLAHITA477 DICGMKLPWL487 YVGMCFSSFC497 WHIEDHWSYS 507 INYLHWGEPK517 TWYGVPGYAA527 EQLENVMKKL537 APELFVSQPD547 LLHQLVTIMN 557 PNTLMTHEVP567 VYRTNQCAGE577 FVITFPRAYH587 SGFNQGFNFA597 EAVNFCTVDW 607 LPLGRQCVEH617 YRLLHRYCVF627 SHDEMICKMA637 SKADVLDVVV647 ASTVQKDMAI 657 MIEDEKALRE667 TVRKLGVIDS677 ERMDFELLPD687 DERQCVKCKT697 TCFMSAISCS 707 CKPGLLVCLH717 HVKELCSCPP727 YKYKLRYRYT737 LDDLYPMMNA747 LKLRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LQT or .LQT2 or .LQT3 or :3LQT;style chemicals stick;color identity;select .A:98 or .A:99 or .A:425 or .A:481 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:502 or .A:507 or .A:509 or .A:517 or .A:519 or .A:587 or .A:597 or .A:599 or .A:600 or .A:601; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Pyridine-2,4-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human PLU-1 (JARID1B) in complex with Pyridine-2, 6-dicarboxylic Acid (PDCA) | PDB:5A3W | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKARD376 YTLRTFGEMA386 DAFKSDYFNM396 PVHMVPTELV 406 EKEFWRLVST416 IEEDVTVEYG426 ADIASKEFGS436 GFPVRDIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PD2 or .PD22 or .PD23 or :3PD2;style chemicals stick;color identity;select .A:98 or .A:425 or .A:488 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: GSK-J1 | Ligand Info | |||||
| Structure Description | Crystal structure of human JARID1B in complex with GSKJ1 | PDB:5FPU | ||||
| Method | X-ray diffraction | Resolution | 2.24 Å | Mutation | No | [4] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .K0I or .K0I2 or .K0I3 or :3K0I;style chemicals stick;color identity;select .A:88 or .A:96 or .A:97 or .A:98 or .A:99 or .A:100 or .A:425 or .A:427 or .A:488 or .A:495 or .A:496 or .A:497 or .A:499 or .A:500 or .A:501 or .A:502 or .A:509 or .A:517 or .A:519 or .A:553 or .A:587 or .A:597; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLN88
3.563
GLN96
3.327
THR97
2.995
ARG98
3.407
VAL99
4.190
LYS100
3.997
TYR425
3.329
ALA427
4.134
TYR488
3.507
SER495
3.289
PHE496
3.464
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| Ligand Name: Alpha-ketoglutaric acid | Ligand Info | |||||
| Structure Description | Crystal structure of human JARID1B in complex with 2-oxoglutarate. | PDB:5FUP | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [4] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVRDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDIKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITADIC480 GMKLPWLYVG490 MCFSSFCWHI500 EDHWSYSINY 510 LHWGEPKTWY520 GVPGYAAEQL530 ENVMKKLAPE540 LFVSQPDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAES |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AKG or .AKG2 or .AKG3 or :3AKG;style chemicals stick;color identity;select .A:425 or .A:488 or .A:496 or .A:499 or .A:501 or .A:507 or .A:508 or .A:509 or .A:517 or .A:519 or .A:581 or .A:587 or .A:597 or .A:599; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Isonipecotic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment N05859b (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZ6 | ||||
| Method | X-ray diffraction | Resolution | 2.33 Å | Mutation | No | [5] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MN1 or .MN12 or .MN13 or :3MN1;style chemicals stick;color identity;select .A:488 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587 or .A:597; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(carboxymethylamino)-2-oxoacetic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of PLU1 in complex with N-oxalylglycine. | PDB:5A1F | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [4] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVRDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDSPEEEE453 YLDSGWNLNN 463 MPVMEQSVLA473 HITADICGMK483 LPWLYVGMCF493 SSFCWHIEDH503 WSYSINYLHW 513 GEPKTWYGVP523 GYAAEQLENV533 MKKLAPELFV543 SQPDLLHQLV553 TIMNPNTLMT 563 HEVPVYRTNQ573 CAGEFVITFP583 RAYHSGFNQG593 FNFAEAVNFC603 TVDWLPLGRQ 613 CVEHYRLLHR623 YCVFSHDEMI633 CKMASKADVL643 DVVVASTVQK653 DMAIMIEDEK 663 ALRETVRKLG673 VIDSERMDFE683 LLPDDERQCV693 KCKTTCFMSA703 ISCSCKPGLL 713 VCLHHVKELC723 SCPPYKYKLR733 YRYTLDDLYP743 MMNALKLRAE753 |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OGA or .OGA2 or .OGA3 or :3OGA;style chemicals stick;color identity;select .A:488 or .A:496 or .A:499 or .A:501 or .A:507 or .A:508 or .A:509 or .A:517 or .A:519 or .A:581 or .A:587 or .A:597 or .A:599; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-{[(2-{[(E)-2-(Dimethylamino)ethenyl](Ethyl)amino}-2-Oxoethyl)amino]methyl}pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human PLU-1 (JARID1B) in complex with KDM5-C49 (2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl) isonicotinic acid). | PDB:5A3T | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [4] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MMK or .MMK2 or .MMK3 or :3MMK;style chemicals stick;color identity;select .A:98 or .A:99 or .A:425 or .A:428 or .A:480 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:502 or .A:507 or .A:509 or .A:517 or .A:519 or .A:587 or .A:597 or .A:599 or .A:600 or .A:601; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 8-[4-[2-(4-propanoylpiperazin-1-yl)ethyl]pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of KDM5B in complex with S49365a. | PDB:6EIN | ||||
| Method | X-ray diffraction | Resolution | 2.11 Å | Mutation | No | [6] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AARDYTLRTF382 GEMADAFKSD392 YFNMPVHMVP402 TELVEKEFWR 412 LVSTIEEDVT422 VEYGADIASK432 EFGSGFPVRD442 KLSPEEEEYL455 DSGWNLNNMP 465 VMEQSVLAHI475 TADICGMKLP485 WLYVGMCFSS495 FCWHIEDHWS505 YSINYLHWGE 515 PKTWYGVPGY525 AAEQLENVMK535 KLAPELLVTI555 MNPNTLMTHE565 VPVYRTNQCA 575 GEFVITFPRA585 YHSGFNQGFN595 FAEAVNFCTV605 DWLPLGRQCV615 EHYRLLHRYC 625 VFSHDEMICK635 MASKADVLDV645 VVASTVQKDM655 AIMIEDEKAL665 RETVRKLGVI 675 DSERMDFELL685 PDDERQCVKC695 KTTCFMSAIS705 CSCKPGLLVC715 LHHVKELCSC 725 PPYKYKLRYR735 YTLDDLYPMM745 NALKLRAES
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B7Z or .B7Z2 or .B7Z3 or :3B7Z;style chemicals stick;color identity;select .A:425 or .A:428 or .A:480 or .A:481 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:502 or .A:509 or .A:517 or .A:519 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 8-[4-(1-cyclopentylpiperidin-4-yl)pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM5B in complex with compound 34g | PDB:6H52 | ||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | No | [7] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGKIKL447 SPEEEEYLDS 457 GWNLNNMPVM467 EQSVLAHITA477 DICGMKLPWL487 YVGMCFSSFC497 WHIEDHWSYS 507 INYLHWGEPK517 TWYGVPGYAA527 EQLENVMKKL537 APELFVSQPD547 LLHQLVTIMN 557 PNTLMTHEVP567 VYRTNQCAGE577 FVITFPRAYH587 SGFNQGFNFA597 EAVNFCTVDW 607 LPLGRQCVEH617 YRLLHRYCVF627 SHDEMICKMA637 SKADVLDVVV647 ASTVQKDMAI 657 MIEDEKALRE667 TVRKLGVIDS677 ERMDFELLPD687 DERQCVKCKT697 TCFMSAISCS 707 CKPGLLVCLH717 HVKELCSCPP727 YKYKLRYRYT737 LDDLYPMMNA747 LKLRAESY |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQN or .FQN2 or .FQN3 or :3FQN;style chemicals stick;color identity;select .A:98 or .A:99 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:502 or .A:509 or .A:517 or .A:519 or .A:587; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM5B in complex with compound 34a | PDB:6H50 | ||||
| Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | No | [7] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAES |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FO2 or .FO22 or .FO23 or :3FO2;style chemicals stick;color identity;select .A:99 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:502 or .A:509 or .A:517 or .A:519 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol | Ligand Info | |||||
| Structure Description | Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol | PDB:6RBI | ||||
| Method | X-ray diffraction | Resolution | 2.21 Å | Mutation | No | [8] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRVKLRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITADIC480 GMKLPWLYVG490 MCFSSFCWHI500 EDHWSYSINY 510 LHWGEPKTWY520 GVPGYAAEQL530 ENVMKKLAPE540 LFVSQPDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAES |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JX8 or .JX82 or .JX83 or :3JX8;style chemicals stick;color identity;select .A:99 or .A:488 or .A:495 or .A:496 or .A:499 or .A:501 or .A:507 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 8-[4-[1-(cyclobutylmethyl)piperidin-4-yl]pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM5B in complex with compound 34f | PDB:6H51 | ||||
| Method | X-ray diffraction | Resolution | 2.21 Å | Mutation | No | [7] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVARDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAES |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQK or .FQK2 or .FQK3 or :3FQK;style chemicals stick;color identity;select .A:98 or .A:425 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:502 or .A:509 or .A:517 or .A:519 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| Ligand Name: 2-[(1-Benzyl-1h-Pyrazol-4-Yl)oxy]pyrido[3,4-D]pyrimidin-4(3h)-One | Ligand Info | |||||
| Structure Description | Crystal structure of human JARID1B in complex with GSK467 | PDB:5FUN | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [4] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVARDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGKKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GZA or .GZA2 or .GZA3 or :3GZA;style chemicals stick;color identity;select .A:86 or .A:88 or .A:97 or .A:98 or .A:425 or .A:427 or .A:486 or .A:488 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human KDM5B in complex with compound 16a | PDB:6H4Z | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [7] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKARD376 YTLRTFGEMA386 DAFKSDYFNM396 PVHMVPTELV 406 EKEFWRLVST416 IEEDVTVEYG426 ADIASKEFGS436 GFPVRDGIKL447 SPEEEEYLDS 457 GWNLNNMPVM467 EQSVLAHITA477 DICGMKLPWL487 YVGMCFSSFC497 WHIEDHWSYS 507 INYLHWGEPK517 TWYGVPGYAA527 EQLENVMKKL537 APELFVSQPD547 LLHQLVTIMN 557 PNTLMTHEVP567 VYRTNQCAGE577 FVITFPRAYH587 SGFNQGFNFA597 EAVNFCTVDW 607 LPLGRQCVEH617 YRLLHRYCVF627 SHDEMICKMA637 SKADVLDVVV647 ASTVQKDMAI 657 MIEDEKALRE667 TVRKLGVIDS677 ERMDFELLPD687 DERQCVKCKT697 TCFMSAISCS 707 CKPGLLVCLH717 HVKELCSCPP727 YKYKLRYRYT737 LDDLYPMMNA747 LKLRAESY |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FQ5 or .FQ52 or .FQ53 or :3FQ5;style chemicals stick;color identity;select .A:31 or .A:32 or .A:33 or .A:55 or .A:58 or .A:59 or .A:98 or .A:99 or .A:425 or .A:428 or .A:481 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:525 or .A:569 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU31
3.580
CYS32
4.062
PRO33
3.835
ILE55
3.855
GLN58
3.075
THR59
3.814
ARG98
3.745
VAL99
4.203
TYR425
2.902
ASP428
3.245
GLY481
4.470
|
|||||
| Ligand Name: 8-[4-[2-[4-[3,5-Bis(Chloranyl)phenyl]piperidin-1-Yl]ethyl]pyrazol-1-Yl]-3~{h}-Pyrido[3,4-D]pyrimidin-4-One | Ligand Info | |||||
| Structure Description | Crystal structure of human JARID1B in complex with S40563a | PDB:5LW9 | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [9] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRVKARDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAES |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5UJ or .5UJ2 or .5UJ3 or :35UJ;style chemicals stick;color identity;select .A:98 or .A:99 or .A:425 or .A:427 or .A:428 or .A:479 or .A:480 or .A:481 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:502 or .A:509 or .A:517 or .A:519 or .A:587; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 8-[4-(2-azanylethyl)pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of human JARID1B in complex with CCT363901 | PDB:5FPL | ||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | No | [10] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRVKARDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PKLFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAES |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QAY or .QAY2 or .QAY3 or :3QAY;style chemicals stick;color identity;select .A:98 or .A:425 or .A:427 or .A:428 or .A:486 or .A:488 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: [(3s)-2-Oxo-2,3-Dihydro-1h-Indol-3-Yl]acetonitrile | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 2-(2-oxo-2,3-dihydro-1H-indol-3-yl)acetonitrile (N10063a) | PDB:5FYZ | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [11] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKLDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NYK or .NYK2 or .NYK3 or :3NYK;style chemicals stick;color identity;select .A:99 or .A:425 or .A:488 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591 or .A:597; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (2S)-2-Hydroxybutanedioic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with malate | PDB:5FZ8 | ||||
| Method | X-ray diffraction | Resolution | 1.86 Å | Mutation | No | [12] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVDYTL379 RTFGEMADAF389 KSDYFNMPVH399 MVPTELVEKE 409 FWRLVSTIEE419 DVTVEYGADI429 ASKEFGSGFP439 VRDIKLSPEE451 EEYLDSGWNL 461 NNMPVMEQSV471 LAHITADICG481 MKLPWLYVGM491 CFSSFCWHIE501 DHWSYSINYL 511 HWGEPKTWYG521 VPGYAAEQLE531 NVMKKLAPEL541 FVSQPDLLHQ551 LVTIMNPNTL 561 MTHEVPVYRT571 NQCAGEFVIT581 FPRAYHSGFN591 QGFNFAEAVN601 FCTVDWLPLG 611 RQCVEHYRLL621 HRYCVFSHDE631 MICKMASKAD641 VLDVVVASTV651 QKDMAIMIED 661 EKALRETVRK671 LGVIDSERMD681 FELLPDDERQ691 CVKCKTTCFM701 SAISCSCKPG 711 LLVCLHHVKE721 LCSCPPYKYK731 LRYRYTLDDL741 YPMMNALKLR751 AES |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LMR or .LMR2 or .LMR3 or :3LMR;style chemicals stick;color identity;select .A:488 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587 or .A:597; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-[(3s)-5-Fluoranyl-2-Oxidanylidene-1,3-Dihydroindol-3-Yl]ethanoic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment (5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl)acetic acid (N09996a) | PDB:5FYT | ||||
| Method | X-ray diffraction | Resolution | 1.87 Å | Mutation | No | [13] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKLRD376 YTLRTFGEMA386 DAFKSDYFNM396 PVHMVPTELV 406 EKEFWRLVST416 IEEDVTVEYG426 ADIASKEFGS436 GFPVRDIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WQS or .WQS2 or .WQS3 or :3WQS;style chemicals stick;color identity;select .A:99 or .A:488 or .A:495 or .A:496 or .A:499 or .A:501 or .A:507 or .A:509 or .A:517 or .A:519 or .A:587 or .A:597 or .A:599; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: N-Hydroxy-3-[(6-Oxo-4-Phenyl-1,6-Dihydropyrimidin-2-Yl)sulfanyl]propanamide | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with MC1648 | PDB:5FYB | ||||
| Method | X-ray diffraction | Resolution | 1.87 Å | Mutation | No | [14] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKLRD376 YTLRTFGEMA386 DAFKSDYFNM396 PVHMVPTELV 406 EKEFWRLVST416 IEEDVTVEYG426 ADIASKEFGS436 GFPVRDIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .77J or .77J2 or .77J3 or :377J;style chemicals stick;color identity;select .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:55 or .A:59 or .A:99 or .A:425 or .A:427 or .A:488 or .A:489 or .A:490 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:507 or .A:509 or .A:517 or .A:519 or .A:569 or .A:581 or .A:587 or .A:591 or .A:597 or .A:599; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU31
3.140
CYS32
3.578
PRO33
3.416
VAL34
2.904
PHE35
3.813
ILE55
3.305
THR59
3.748
VAL99
3.778
TYR425
3.931
ALA427
4.293
TYR488
3.379
VAL489
4.869
GLY490
4.224
SER494
4.272
|
|||||
| Ligand Name: (2R)-2-hydroxypentanedioic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with D-2-hydroxyglutarate | PDB:5FYS | ||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | No | [15] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDIKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITADIC480 GMKLPWLYVG490 MCFSSFCWHI500 EDHWSYSINY 510 LHWGEPKTWY520 GVPGYAAEQL530 ENVMKKLAPE540 LFVSQPDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2HG or .2HG2 or .2HG3 or :32HG;style chemicals stick;color identity;select .A:98 or .A:488 or .A:496 or .A:499 or .A:501 or .A:507 or .A:508 or .A:509 or .A:517 or .A:519 or .A:581 or .A:587 or .A:599; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 6-Oxo-2-[(2-Oxo-2-Phenylethyl)sulfanyl]-1,6-Dihydropyrimidine-5-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with MC3095 | PDB:5FZI | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [16] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKLGG103 GGARDYTLRT381 FGEMADAFKS391 DYFNMPVHMV 401 PTELVEKEFW411 RLVSTIEEDV421 TVEYGADIAS431 KEFGSGFPVR441 DGIKLSPEEE 452 EYLDSGWNLN462 NMPVMEQSVL472 AHITADICGM482 KLPWLYVGMC492 FSSFCWHIED 502 HWSYSINYLH512 WGEPKTWYGV522 PGYAAEQLEN532 VMKKLAPELF542 VSQPDLLHQL 552 VTIMNPNTLM562 THEVPVYRTN572 QCAGEFVITF582 PRAYHSGFNQ592 GFNFAEAVNF 602 CTVDWLPLGR612 QCVEHYRLLH622 RYCVFSHDEM632 ICKMASKADV642 LDVVVASTVQ 652 KDMAIMIEDE662 KALRETVRKL672 GVIDSERMDF682 ELLPDDERQC692 VKCKTTCFMS 702 AISCSCKPGL712 LVCLHHVKEL722 CSCPPYKYKL732 RYRYTLDDLY742 PMMNALKLRA 752 E
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FIG or .FIG2 or .FIG3 or :3FIG;style chemicals stick;color identity;select .A:98 or .A:99 or .A:425 or .A:427 or .A:488 or .A:495 or .A:496 or .A:499 or .A:500 or .A:501 or .A:502 or .A:509 or .A:517 or .A:551 or .A:553 or .A:591; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (4-Oxo-6-phenyl-1,4-dihydro-pyrimidin-2-YL-sulfanyl)-acetic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with MC3948 | PDB:5FZG | ||||
| Method | X-ray diffraction | Resolution | 1.96 Å | Mutation | No | [17] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKARD376 YTLRTFGEMA386 DAFKSDYFNM396 PVHMVPTELV 406 EKEFWRLVST416 IEEDVTVEYG426 ADIASKEFGS436 GFPVRDIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7IA or .7IA2 or .7IA3 or :37IA;style chemicals stick;color identity;select .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:55 or .A:59 or .A:86 or .A:98 or .A:425 or .A:427 or .A:488 or .A:490 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:569 or .A:587 or .A:591 or .A:599; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU31
3.228
CYS32
3.599
PRO33
3.376
VAL34
2.862
PHE35
3.959
ILE55
3.544
THR59
3.732
ARG86
4.388
ARG98
3.081
TYR425
3.636
ALA427
3.975
TYR488
3.400
GLY490
4.640
|
|||||
| Ligand Name: N-Hydroxy-2-[(6-Oxo-4-Phenyl-1,6-Dihydropyrimidin-2-Yl)sulfanyl]acetamide | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with MC3962 | PDB:5FZF | ||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | No | [18] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGKIKL447 SPEEEEYLDS 457 GWNLNNMPVM467 EQSVLAHITA477 DICGMKLPWL487 YVGMCFSSFC497 WHIEDHWSYS 507 INYLHWGEPK517 TWYGVPGYAA527 EQLENVMKKL537 APELFVSQPD547 LLHQLVTIMN 557 PNTLMTHEVP567 VYRTNQCAGE577 FVITFPRAYH587 SGFNQGFNFA597 EAVNFCTVDW 607 LPLGRQCVEH617 YRLLHRYCVF627 SHDEMICKMA637 SKADVLDVVV647 ASTVQKDMAI 657 MIEDEKALRE667 TVRKLGVIDS677 ERMDFELLPD687 DERQCVKCKT697 TCFMSAISCS 707 CKPGLLVCLH717 HVKELCSCPP727 YKYKLRYRYT737 LDDLYPMMNA747 LKLRAES |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UUN or .UUN2 or .UUN3 or :3UUN;style chemicals stick;color identity;select .A:31 or .A:32 or .A:33 or .A:34 or .A:35 or .A:55 or .A:59 or .A:86 or .A:98 or .A:425 or .A:427 or .A:488 or .A:490 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:507 or .A:509 or .A:517 or .A:519 or .A:569 or .A:581 or .A:587 or .A:591 or .A:599; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU31
3.300
CYS32
3.736
PRO33
3.439
VAL34
2.893
PHE35
4.009
ILE55
3.726
THR59
3.738
ARG86
4.237
ARG98
3.438
TYR425
3.696
ALA427
4.078
TYR488
3.275
GLY490
4.841
SER494
4.570
|
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| Ligand Name: [(6-Oxo-4-Phenyl-1,6-Dihydropyrimidin-2-Yl)sulfanyl]acetonitrile | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with MC3960 | PDB:5FZE | ||||
| Method | X-ray diffraction | Resolution | 2.02 Å | Mutation | No | [19] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGKIKL447 SPEEEEYLDS 457 GWNLNNMPVM467 EQSVLAHITA477 DICGMKLPWL487 YVGMCFSSFC497 WHIEDHWSYS 507 INYLHWGEPK517 TWYGVPGYAA527 EQLENVMKKL537 APELFVSQPD547 LLHQLVTIMN 557 PNTLMTHEVP567 VYRTNQCAGE577 FVITFPRAYH587 SGFNQGFNFA597 EAVNFCTVDW 607 LPLGRQCVEH617 YRLLHRYCVF627 SHDEMICKMA637 SKADVLDVVV647 ASTVQKDMAI 657 MIEDEKALRE667 TVRKLGVIDS677 ERMDFELLPD687 DERQCVKCKT697 TCFMSAISCS 707 CKPGLLVCLH717 HVKELCSCPP727 YKYKLRYRYT737 LDDLYPMMNA747 LKLRAES |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .H0X or .H0X2 or .H0X3 or :3H0X;style chemicals stick;color identity;select .A:98 or .A:425 or .A:427 or .A:488 or .A:490 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591 or .A:599; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: (2S)-2-hydroxypentanedioic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with L-2-hydroxyglutarate | PDB:5FZD | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [20] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVDYTL379 RTFGEMADAF389 KSDYFNMPVH399 MVPTELVEKE 409 FWRLVSTIEE419 DVTVEYGADI429 ASKEFGSGFP439 VRDIKLSPEE451 EEYLDSGWNL 461 NNMPVMEQSV471 LAHITADICG481 MKLPWLYVGM491 CFSSFCWHIE501 DHWSYSINYL 511 HWGEPKTWYG521 VPGYAAEQLE531 NVMKKLAPEL541 FVSQPDLLHQ551 LVTIMNPNTL 561 MTHEVPVYRT571 NQCAGEFVIT581 FPRAYHSGFN591 QGFNFAEAVN601 FCTVDWLPLG 611 RQCVEHYRLL621 HRYCVFSHDE631 MICKMASKAD641 VLDVVVASTV651 QKDMAIMIED 661 EKALRETVRK671 LGVIDSERMD681 FELLPDDERQ691 CVKCKTTCFM701 SAISCSCKPG 711 LLVCLHHVKE721 LCSCPPYKYK731 LRYRYTLDDL741 YPMMNALKLR751 AE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .S2G or .S2G2 or .S2G3 or :3S2G;style chemicals stick;color identity;select .A:488 or .A:496 or .A:499 or .A:501 or .A:507 or .A:508 or .A:509 or .A:517 or .A:519 or .A:581 or .A:587 or .A:599; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Benzo[g][1]benzothiole-2-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4,5-dihydronaphtho(1,2-b)thiophene-2- carboxylicacid (N11181a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZC | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [21] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDIKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITADIC480 GMKLPWLYVG490 MCFSSFCWHI500 EDHWSYSINY 510 LHWGEPKTWY520 GVPGYAAEQL530 ENVMKKLAPE540 LFVSQPDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .D8S or .D8S2 or .D8S3 or :3D8S;style chemicals stick;color identity;select .A:31 or .A:32 or .A:33 or .A:55 or .A:58 or .A:59 or .A:569; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N,3-Dimethyl-N-[(Pyridin-3-Yl)methyl]-1,2-Oxazole-5-Carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZK | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [22] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NRW or .NRW2 or .NRW3 or :3NRW;style chemicals stick;color identity;select .A:86 or .A:88 or .A:96 or .A:97 or .A:98 or .A:425 or .A:427 or .A:488 or .A:495 or .A:496 or .A:497 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:553 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: (3r)-3-Azanyl-4-Methyl-1,3-Dihydroindol-2-One | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 3-Amino-4-methyl-1,3-dihydro-2H-indol-2-one (N10042a) | PDB:5FYU | ||||
| Method | X-ray diffraction | Resolution | 2.06 Å | Mutation | No | [23] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKLRD376 YTLRTFGEMA386 DAFKSDYFNM396 PVHMVPTELV 406 EKEFWRLVST416 IEEDVTVEYG426 ADIASKEFGS436 GFPVRDGIKL447 SPEEEEYLDS 457 GWNLNNMPVM467 EQSVLAHITA477 DICGMKLPWL487 YVGMCFSSFC497 WHIEDHWSYS 507 INYLHWGEPK517 TWYGVPGYAA527 EQLENVMKKL537 APELFVSQPD547 LLHQLVTIMN 557 PNTLMTHEVP567 VYRTNQCAGE577 FVITFPRAYH587 SGFNQGFNFA597 EAVNFCTVDW 607 LPLGRQCVEH617 YRLLHRYCVF627 SHDEMICKMA637 SKADVLDVVV647 ASTVQKDMAI 657 MIEDEKALRE667 TVRKLGVIDS677 ERMDFELLPD687 DERQCVKCKT697 TCFMSAISCS 707 CKPGLLVCLH717 HVKELCSCPP727 YKYKLRYRYT737 LDDLYPMMNA747 LKLRAES |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BY4 or .BY42 or .BY43 or :3BY4;style chemicals stick;color identity;select .A:99 or .A:425 or .A:426 or .A:427 or .A:488 or .A:495 or .A:496 or .A:499 or .A:509 or .A:517 or .A:519 or .A:591 or .A:597; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Thieno[3,2-b]thiophene-2-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment thieno(3,2-b)thiophene-5-carboxylic acid (N06263b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZ9 | ||||
| Method | X-ray diffraction | Resolution | 2.06 Å | Mutation | No | [24] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NUK or .NUK2 or .NUK3 or :3NUK;style chemicals stick;color identity;select .A:53 or .A:57 or .A:98 or .A:425 or .A:426 or .A:427 or .A:488 or .A:490 or .A:494 or .A:495 or .A:496 or .A:506 or .A:509 or .A:517 or .A:582 or .A:583 or .A:591 or .A:606 or .A:607 or .A:609 or .A:610 or .A:613 or .A:659 or .A:662 or .A:663 or .A:666 or .A:701 or .A:736 or .A:737 or .A:738 or .A:741; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG53
3.145
GLU57
3.001
ARG98
3.919
TYR425
3.431
GLY426
4.939
ALA427
4.146
TYR488
3.352
GLY490
4.878
SER494
4.741
SER495
4.500
PHE496
3.690
TYR506
3.262
ASN509
4.631
LYS517
2.936
PHE582
3.899
PRO583
3.441
|
|||||
| Ligand Name: (3s)-1-[(3-Phenyl-1,2,4-Oxadiazol-5-Yl)methyl]pyrrolidin-3-Ol | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment (3R)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol (N10057a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZ4 | ||||
| Method | X-ray diffraction | Resolution | 2.07 Å | Mutation | No | [25] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDIKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITAICG481 MKLPWLYVGM491 CFSSFCWHIE501 DHWSYSINYL 511 HWGEPKTWYG521 VPGYAAEQLE531 NVMKKLAPEL541 FVSQPDLLHQ551 LVTIMNPNTL 561 MTHEVPVYRT571 NQCAGEFVIT581 FPRAYHSGFN591 QGFNFAEAVN601 FCTVDWLPLG 611 RQCVEHYRLL621 HRYCVFSHDE631 MICKMASKAD641 VLDVVVASTV651 QKDMAIMIED 661 EKALRETVRK671 LGVIDSERMD681 FELLPDDERQ691 CVKCKTTCFM701 SAISCSCKPG 711 LLVCLHHVKE721 LCSCPPYKYK731 LRYRYTLDDL741 YPMMNALKLR751 AE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P6B or .P6B2 or .P6B3 or :3P6B;style chemicals stick;color identity;select .A:659 or .A:662 or .A:663 or .A:666 or .A:667 or .A:670 or .A:701 or .A:736 or .A:737 or .A:738 or .A:741; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (3r)-5-Fluoro-3-Hydroxy-1,3-Dihydro-2h-Indol-2-One | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4,5-dihydronaphtho(1,2-b)thiophene-2- carboxylicacid (N11181a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZH | ||||
| Method | X-ray diffraction | Resolution | 2.09 Å | Mutation | No | [26] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKLGG103 GGARDYTLRT381 FGEMADAFKS391 DYFNMPVHMV 401 PTELVEKEFW411 RLVSTIEEDV421 TVEYGADIAS431 KEFGSGFPVR441 DIKLSPEEEE 453 YLDSGWNLNN463 MPVMEQSVLA473 HITADICGMK483 LPWLYVGMCF493 SSFCWHIEDH 503 WSYSINYLHW513 GEPKTWYGVP523 GYAAEQLENV533 MKKLAPELFV543 SQPDLLHQLV 553 TIMNPNTLMT563 HEVPVYRTNQ573 CAGEFVITFP583 RAYHSGFNQG593 FNFAEAVNFC 603 TVDWLPLGRQ613 CVEHYRLLHR623 YCVFSHDEMI633 CKMASKADVL643 DVVVASTVQK 653 DMAIMIEDEK663 ALRETVRKLG673 VIDSERMDFE683 LLPDDERQCV693 KCKTTCFMSA 703 ISCSCKPGLL713 VCLHHVKELC723 SCPPYKYKLR733 YRYTLDDLYP743 MMNALKLRAE 753
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0TI or .0TI2 or .0TI3 or :30TI;style chemicals stick;color identity;select .A:99 or .A:425 or .A:427 or .A:488 or .A:495 or .A:496 or .A:499 or .A:509 or .A:517 or .A:519 or .A:591 or .A:597; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)pyridine | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 2-piperidin-4-yloxy-5-(trifluoromethyl)pyridine (N10072a) (ligand modelled based on PANDDA event map) | PDB:5FZA | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [27] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDIKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITADIC480 GMKLPWLYVG490 MCFSSFCWHI500 EDHWSYSINY 510 LHWGEPKTWY520 GVPGYAAEQL530 ENVMKKLAPE540 LFVSQPDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .80Q or .80Q2 or .80Q3 or :380Q;style chemicals stick;color identity;select .A:658 or .A:659 or .A:662 or .A:663 or .A:666 or .A:667 or .A:701 or .A:736 or .A:737 or .A:738 or .A:741; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3-(Pyridin-3-yl)benzenamine | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3-pyridin-3-ylaniline (N05798a) (ligand modelled based on PANDDA event map) | PDB:5FYY | ||||
| Method | X-ray diffraction | Resolution | 2.18 Å | Mutation | No | [28] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKKDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N6Y or .N6Y2 or .N6Y3 or :3N6Y;style chemicals stick;color identity;select .A:99 or .A:425 or .A:427 or .A:488 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-Pyridylthiourea | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4-Pyridylthiourea (N06275b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZB | ||||
| Method | X-ray diffraction | Resolution | 2.18 Å | Mutation | No | [29] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRLKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .YS6 or .YS62 or .YS63 or :3YS6;style chemicals stick;color identity;select .A:488 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591 or .A:597; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Ethyl 2-Amino-4-(2-thienyl)thiophene-3-carboxylate | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment ethyl 2-amino-4-thiophen-2-ylthiophene-3- carboxylate (N06131b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZ7 | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [30] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKARD376 YTLRTFGEMA386 DAFKSDYFNM396 PVHMVPTELV 406 EKEFWRLVST416 IEEDVTVEYG426 ADIASKEFGS436 GFPVRDIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WGT or .WGT2 or .WGT3 or :3WGT;style chemicals stick;color identity;select .A:99 or .A:425 or .A:426 or .A:427 or .A:488 or .A:489 or .A:490 or .A:494 or .A:495 or .A:496 or .A:509 or .A:517 or .A:519 or .A:591 or .A:597; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2,4-dichloro-N-(pyridin-3-yl)benzamide | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 2,4-dichloro-N-pyridin-3-ylbenzamide (E48115b) (ligand modelled based on PANDDA event map) | PDB:5FZ1 | ||||
| Method | X-ray diffraction | Resolution | 2.39 Å | Mutation | No | [31] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDGIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .W77 or .W772 or .W773 or :3W77;style chemicals stick;color identity;select .A:86 or .A:88 or .A:98 or .A:99 or .A:100 or .A:425 or .A:427 or .A:486 or .A:488 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:519 or .A:587; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2,5-Dichloro-N-(Pyridin-3-Yl)thiophene-3-Carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 2,5-dichloro-N-(pyridin-3-yl)thiophene-3-carboxamide (N08137b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZ0 | ||||
| Method | X-ray diffraction | Resolution | 2.42 Å | Mutation | No | [32] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVRDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDIKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITADIC480 GMKLPWLYVG490 MCFSSFCWHI500 EDHWSYSINY 510 LHWGEPKTWY520 GVPGYAAEQL530 ENVMKKLAPE540 LFVSQPDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DJ6 or .DJ62 or .DJ63 or :3DJ6;style chemicals stick;color identity;select .A:86 or .A:88 or .A:98 or .A:99 or .A:425 or .A:427 or .A:486 or .A:488 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:519 or .A:587; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-(2-Fluorophenyl)-1,3-oxazole-4-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 5-(2-fluorophenyl)-1,3-oxazole-4-carboxylic acid (N09989b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZM | ||||
| Method | X-ray diffraction | Resolution | 2.49 Å | Mutation | No | [33] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKSDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P60 or .P602 or .P603 or :3P60;style chemicals stick;color identity;select .A:98 or .A:99 or .A:425 or .A:427 or .A:486 or .A:488 or .A:495 or .A:496 or .A:499 or .A:501 or .A:519 or .A:587; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (1r,4s)-1,2,3,4-Tetrahydro-1,4-Methanonaphthalene-5,8-Diol | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3,6-Dihydroxybenzonorbornane (N08776b) (ligand modelled based on PANDDA event map) | PDB:5FZ3 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [34] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVRDYT378 LRTFGEMADA388 FKSDYFNMPV398 HMVPTELVEK 408 EFWRLVSTIE418 EDVTVEYGAD428 IASKEFGSGF438 PVRDIKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITADIC480 GMKLPWLYVG490 MCFSSFCWHI500 EDHWSYSINY 510 LHWGEPKTWY520 GVPGYAAEQL530 ENVMKKLAPE540 LFVSQPDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7SI or .7SI2 or .7SI3 or :37SI;style chemicals stick;color identity;select .A:29 or .A:30 or .A:562 or .A:565 or .A:566 or .A:567 or .A:568 or .A:569; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-Methyl-N-(Pyridin-4-Yl)-1,2-Oxazole-5-Carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 3-methyl-N-pyridin-4-yl-1,2-oxazole-5-carboxamide (N09954a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) | PDB:5FZL | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [35] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPLHQ551 LVTIMNPNTL 561 MTHEVPVYRT571 NQCAGEFVIT581 FPRAYHSGFN591 QGFNFAEAVN601 FCTVDWLPLG 611 RQCVEHYRLL621 HRYCVFSHDE631 MICKMASKAD641 VLDVVVASTV651 QKDMAIMIED 661 EKALRETVRK671 LGVIDSERMD681 FELLPDDERQ691 CVKCKTTCFM701 SAISCSCKPG 711 LLVCLHHVKE721 LCSCPPYKYK731 LRYRYTLDDL741 YPMMNALKLR751 AE |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UOI or .UOI2 or .UOI3 or :3UOI;style chemicals stick;color identity;select .A:88 or .A:425 or .A:426 or .A:488 or .A:489 or .A:490 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591 or .A:597; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 8-Oxidanyl-6-phenyl-7-propan-2-yl-imidazo[1,2-b]pyridazine-3-carbonitrile | Ligand Info | |||||
| Structure Description | Crystal structure of KDM5B in complex with KDOPZ29a | PDB:6EIU | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [36] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRVKARDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRIKLSPE450 EEEYLDSGWN 460 LNNMPVMEQS470 VLAHITADIC480 GMKLPWLYVG490 MCFSSFCWHI500 EDHWSYSINY 510 LHWGEPKTWY520 GVPGYAAEQL530 ENVMKKLAPE540 LFVSQPDLLH550 QLVTIMNPNT 560 LMTHEVPVYR570 TNQCAGEFVI580 TFPRAYHSGF590 NQGFNFAEAV600 NFCTVDWLPL 610 GRQCVEHYRL620 LHRYCVFSHD630 EMICKMASKA640 DVLDVVVAST650 VQKDMAIMIE 660 DEKALRETVR670 KLGVIDSERM680 DFELLPDDER690 QCVKCKTTCF700 MSAISCSCKP 710 GLLVCLHHVK720 ELCSCPPYKY730 KLRYRYTLDD740 LYPMMNALKL750 RAES |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B6T or .B6T2 or .B6T3 or :3B6T;style chemicals stick;color identity;select .A:86 or .A:98 or .A:425 or .A:426 or .A:427 or .A:488 or .A:489 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 2-chloranyl-~{N}-[2-[4-(3-cyano-7-oxidanylidene-6-propan-2-yl-4~{H}-pyrazolo[1,5-a]pyrimidin-5-yl)pyrazol-1-yl]ethyl]ethanamide | Ligand Info | |||||
| Structure Description | Crystal structure of KDM5B in complex with KDOPZ000034a. | PDB:6EIY | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [37] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRVKARDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDGIKLS448 PEEEEYLDSG 458 WNLNNMPVME468 QSVLAHITAD478 ICGMKLPWLY488 VGMCFSSFCW498 HIEDHWSYSI 508 NYLHWGEPKT518 WYGVPGYAAE528 QLENVMKKLA538 PELFVSQPDL548 LHQLVTIMNP 558 NTLMTHEVPV568 YRTNQCAGEF578 VITFPRAYHS588 GFNQGFNFAE598 AVNFCTVDWL 608 PLGRQCVEHY618 RLLHRYCVFS628 HDEMICKMAS638 KADVLDVVVA648 STVQKDMAIM 658 IEDEKALRET668 VRKLGVIDSE678 RMDFELLPDD688 ERQCVKCKTT698 CFMSAISCSC 708 KPGLLVCLHH718 VKELCSCPPY728 KYKLRYRYTL738 DDLYPMMNAL748 KLRAES |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B6W or .B6W2 or .B6W3 or :3B6W;style chemicals stick;color identity;select .A:88 or .A:96 or .A:97 or .A:98 or .A:99 or .A:425 or .A:426 or .A:427 or .A:488 or .A:489 or .A:490 or .A:494 or .A:495 or .A:496 or .A:497 or .A:498 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:553 or .A:587 or .A:591; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLN88
3.668
GLN96
3.675
THR97
3.246
ARG98
3.804
VAL99
3.783
TYR425
3.066
GLY426
3.609
ALA427
4.541
TYR488
3.515
VAL489
3.898
GLY490
4.621
SER494
3.782
|
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| Ligand Name: 5-[1-[1-(2-chloranylethanoyl)piperidin-4-yl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-4~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile | Ligand Info | |||||
| Structure Description | Crystal structure of KDM5B in complex with KDOPZ48a. | PDB:6EJ1 | ||||
| Method | X-ray diffraction | Resolution | 2.07 Å | Mutation | No | [38] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRRDYTLR380 TFGEMADAFK390 SDYFNMPVHM400 VPTELVEKEF 410 WRLVSTIEED420 VTVEYGADIA430 SKEFGSGFPV440 RDGIKLSPEE451 EEYLDSGWNL 461 NNMPVMEQSV471 LAHITADICG481 MKLPWLYVGM491 CFSSFCWHIE501 DHWSYSINYL 511 HWGEPKTWYG521 VPGYAAEQLE531 NVMKKLAPEL541 FVSQPDLLHQ551 LVTIMNPNTL 561 MTHEVPVYRT571 NQCAGEFVIT581 FPRAYHSGFN591 QGFNFAEAVN601 FCTVDWLPLG 611 RQCVEHYRLL621 HRYCVFSHDE631 MICKMASKAD641 VLDVVVASTV651 QKDMAIMIED 661 EKALRETVRK671 LGVIDSERMD681 FELLPDDERQ691 CVKCKTTCFM701 SAISCSCKPG 711 LLVCLHHVKE721 LCSCPPYKYK731 LRYRYTLDDL741 YPMMNALKLR751 AES |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B7Q or .B7Q2 or .B7Q3 or :3B7Q;style chemicals stick;color identity;select .A:86 or .A:98 or .A:425 or .A:426 or .A:427 or .A:486 or .A:488 or .A:489 or .A:490 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:502 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: Kdm5A-IN-1 | Ligand Info | |||||
| Structure Description | Crystal structure of KDM5B in complex with S49195a. | PDB:6EK6 | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [39] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRVRDYTL379 RTFGEMADAF389 KSDYFNMPVH399 MVPTELVEKE 409 FWRLVSTIEE419 DVTVEYGADI429 ASFGSGFPVR441 DIKLSPEEEE453 YLDSGWNLNN 463 MPVMEQSVLA473 HITADICGMK483 LPWLYVGMCF493 SSFCWHIEDH503 WSYSINYLHW 513 GEPKTWYGVP523 GYAAEQLENV533 MKKLAPELFV543 SQPDLLHQLV553 TIMNPNTLMT 563 HEVPVYRTNQ573 CAGEFVITFP583 RAYHSGFNQG593 FNFAEAVNFC603 TVDWLPLGRQ 613 CVEHYRLLHR623 YCVFSHDEMI633 CKMASKADVL643 DVVVASTVQK653 DMAIMIEDEK 663 ALRETVRKLG673 VIDSERMDFE683 LLPDDERQCV693 KCKTTCFMSA703 ISCSCKPGLL 713 VCLHHVKELC723 SCPPYKYKLR733 YRYTLDDLYP743 MMNALKLRAE753 S |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .90V or .90V2 or .90V3 or :390V;style chemicals stick;color identity;select .A:425 or .A:426 or .A:486 or .A:488 or .A:489 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:507 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591 or .A:597 or .A:599 or .A:600 or .A:601; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
TYR425
3.618
GLY426
4.298
TRP486
4.161
TYR488
3.151
VAL489
4.629
SER494
4.138
SER495
3.722
PHE496
3.429
HIS499
3.017
GLU501
2.605
|
|||||
| Ligand Name: 5-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile | Ligand Info | |||||
| Structure Description | Crystal structure of human JARID1B in complex with S40650a | PDB:5LWB | ||||
| Method | X-ray diffraction | Resolution | 2.39 Å | Mutation | No | [40] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRVRDYTL379 RTFGEMADAF389 KSDYFNMPVH399 MVPTELVEKE 409 FWRLVSTIEE419 DVTVEYGADI429 ASKEFGSGFP439 VRDIKLSPEE451 EEYLDSGWNL 461 NNMPVMEQSV471 LAHITADICG481 MKLPWLYVGM491 CFSSFCWHIE501 DHWSYSINYL 511 HWGEPKTWYG521 VPGYAAEQLE531 NVMKKLAPEL541 FVSQPDLLHQ551 LVTIMNPNTL 561 MTHEVPVYRT571 NQCAGEFVIT581 FPRAYHSGFN591 QGFNFAEAVN601 FCTVDWLPLG 611 RQCVEHYRLL621 HRYCVFSHDE631 MICKMASKAD641 VLDVVVASTV651 QKDMAIMIED 661 EKALRETVRK671 LGVIDSERMD681 FELLPDDERQ691 CVKCKTTCFM701 SAISCSCKPG 711 LLVCLHHVKE721 LCSCPPYKYK731 LRYRYTLDDL741 YPMMNALKLR751 AE |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .79H or .79H2 or .79H3 or :379H;style chemicals stick;color identity;select .A:88 or .A:96 or .A:97 or .A:98 or .A:425 or .A:426 or .A:427 or .A:488 or .A:489 or .A:490 or .A:494 or .A:495 or .A:496 or .A:497 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:553 or .A:587 or .A:591; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLN88
3.574
GLN96
4.040
THR97
3.448
ARG98
3.675
TYR425
3.110
GLY426
3.332
ALA427
3.984
TYR488
3.378
VAL489
3.842
GLY490
4.753
SER494
3.808
|
|||||
| Ligand Name: 7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile | Ligand Info | |||||
| Structure Description | Crystal structure of KDM5B in complex with KDOPZ000049a. | PDB:6EJ0 | ||||
| Method | X-ray diffraction | Resolution | 2.06 Å | Mutation | No | [41] |
| PDB Sequence |
MFLPPPECPV
34 FEPSWEEFAD44 PFAFIHKIRP54 IAEQTGICKV64 RPPPDWQPPF74 ACDVDKLHFT 84 PRIQRLNELE94 AQTRRDYTLR380 TFGEMADAFK390 SDYFNMPVHM400 VPTELVEKEF 410 WRLVSTIEED420 VTVEYGADIA430 SKEFGSGFPV440 RDGIKLSPEE451 EEYLDSGWNL 461 NNMPVMEQSV471 LAHITADICG481 MKLPWLYVGM491 CFSSFCWHIE501 DHWSYSINYL 511 HWGEPKTWYG521 VPGYAAEQLE531 NVMKKLAPEL541 FVSQPDLLHQ551 LVTIMNPNTL 561 MTHEVPVYRT571 NQCAGEFVIT581 FPRAYHSGFN591 QGFNFAEAVN601 FCTVDWLPLG 611 RQCVEHYRLL621 HRYCVFSHDE631 MICKMASKAD641 VLDVVVASTV651 QKDMAIMIED 661 EKALRETVRK671 LGVIDSERMD681 FELLPDDERQ691 CVKCKTTCFM701 SAISCSCKPG 711 LLVCLHHVKE721 LCSCPPYKYK731 LRYRYTLDDL741 YPMMNALKLR751 AES |
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B7K or .B7K2 or .B7K3 or :3B7K;style chemicals stick;color identity;select .A:86 or .A:97 or .A:98 or .A:425 or .A:426 or .A:427 or .A:486 or .A:488 or .A:489 or .A:490 or .A:494 or .A:495 or .A:496 or .A:499 or .A:501 or .A:509 or .A:517 or .A:519 or .A:587 or .A:591; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Pyruvate | ||||
| REF 2 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Succinate | ||||
| REF 3 | Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. Cell Chem Biol. 2017 Mar 16;24(3):371-380. | ||||
| REF 4 | Structural analysis of human KDM5B guides histone demethylase inhibitor development. Nat Chem Biol. 2016 Jul;12(7):539-45. | ||||
| REF 5 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment N05859B (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) | ||||
| REF 6 | Crystal structure of KDM5B in complex with S49365a. | ||||
| REF 7 | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur J Med Chem. 2019 Sep 1;177:316-337. | ||||
| REF 8 | Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol | ||||
| REF 9 | Crystal structure of human JARID1B in complex with S40563a | ||||
| REF 10 | 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J Med Chem. 2016 Feb 25;59(4):1388-409. | ||||
| REF 11 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N10063A | ||||
| REF 12 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Malate | ||||
| REF 13 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N09996A | ||||
| REF 14 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc1648 | ||||
| REF 15 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with D-2-Hydroxyglutarate | ||||
| REF 16 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc3095 | ||||
| REF 17 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc3948 | ||||
| REF 18 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc3962 | ||||
| REF 19 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc3960 | ||||
| REF 20 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with L-2-Hydroxyglutarate | ||||
| REF 21 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment 4,5-Dihydronaphtho(1,2-B)Thiophene-2-Carboxylicacid (N11181A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) | ||||
| REF 22 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with 3D Fragment N,3-Dimethyl-N-(Pyridin-3-Ylmethyl)-1,2-Oxazole-5-Carboxamide (N10051A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) | ||||
| REF 23 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N10042A | ||||
| REF 24 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment Thieno(3,2-B)Thiophene -5-Carboxylic Acid (N06263B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) | ||||
| REF 25 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N10057A | ||||
| REF 26 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment 4,5-Dihydronaphtho(1,2-B)Thiophene-2-Carboxylicacid (N11181A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) | ||||
| REF 27 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with 3D Fragment 2-Piperidin-4-Yloxy-5-(Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based on Pandda Event Map) | ||||
| REF 28 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N05798A | ||||
| REF 29 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment 4-Pyridylthiourea (N06275B) (Ligand Modelled Based on Pandda Event Map, Sgc -Diamond I04-1 Fragment Screening) | ||||
| REF 30 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment Ethyl 2-Amino-4-Thiophen-2-Ylthiophene-3-Carboxylate (N06131B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) | ||||
| REF 31 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with E48115B | ||||
| REF 32 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N11213A | ||||
| REF 33 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with 3D Fragment 5-(2-Fluorophenyl)-1,3-Oxazole-4-Carboxylic Acid (N09989B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) | ||||
| REF 34 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N08776B | ||||
| REF 35 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with 3D Fragment 3-Methyl-N-Pyridin-4-Yl-1,2-Oxazole-5-Carboxamide (N09954A) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) | ||||
| REF 36 | Crystal structure of KDM5B in complex with KDOPZ29a. | ||||
| REF 37 | Crystal structure of KDM5B in complex with KDOPZ000034a. | ||||
| REF 38 | Crystal structure of KDM5B in complex with KDOPZ48a. | ||||
| REF 39 | Crystal structure of KDM5B in complex with S49195a. | ||||
| REF 40 | Crystal structure of human JARID1B in complex with S40650a | ||||
| REF 41 | Crystal structure of KDM5B in complex with KDOPZ000049a. | ||||
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