Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T16739 | Target Info | |||
| Target Name | Lysine-specific histone demethylase 1 (LSD) | ||||
| Synonyms | Lysine-specific histone demethylase 1A; LSD1; KIAA0601; KDM1; Flavin-containing amine oxidase domain-containing protein 2; BRAF35-HDAC complex protein BHC110; AOF2 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | KDM1A | ||||
| Biochemical Class | CH-NH(2) donor oxidoreductase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 3-[3,5-Bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal | Ligand Info | |||
| Canonical SMILES | C1=CC=C(C=C1)COC2=C(C=C(C=C2F)F)CCC=O | ||||
| InChI | 1S/C16H14F2O2/c17-14-9-13(7-4-8-19)16(15(18)10-14)20-11-12-5-2-1-3-6-12/h1-3,5-6,8-10H,4,7,11H2 | ||||
| InChIKey | SMGWBKIRLMNBMH-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 146018668 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6KGO LSD1-S2157 five-membered ring adduct model | ||||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [1] |
| PDB Sequence |
SGVEGAAFQS
181 RLPHDRMTSQ191 EAACFPDIIS201 GPQQTQKVFL211 FIRNRTLQLW221 LDNPKIQLTF 231 EATLQQLEAP241 YNSDTVLVHR251 VHSYLERHGL261 INFGIYKRIK271 PLPTKKTGKV 281 IIIGSGVSGL291 AAARQLQSFG301 MDVTLLEARD311 RVGGRVATFR321 KGNYVADLGA 331 MVVTGLGGNP341 MAVVSKQVNM351 ELAKIKQKCP361 LYEANGQAVP371 KEKDEMVEQE 381 FNRLLEATSY391 LSHQLDFNVL401 NNKPVSLGQA411 LEVVIQLQEK421 HVKDEQIEHW 431 KKIVKTQEEL441 KELLNKMVNL451 KEKIKELHQQ461 YKEADITAEF478 LVKSKHRDLT 488 ALCKEYDELA498 ETQGKLEEKL508 QELEANPPSD518 VYLSSRDRQI528 LDWHFANLEF 538 ANATPLSTLS548 LKHWDQDDDF558 EFTGSHLTVR568 NGYSCVPVAL578 AEGLDIKLNT 588 AVRQVRYTAS598 GCEVIAVNTR608 STSQTFIYKC618 DAVLCTLPLG628 VLKQQPPAVQ 638 FVPPLPEWKT648 SAVQRMGFGN658 LNKVVLCFDR668 VFWDPSVNLF678 GHVGSTTASR 688 GELFLFWNLY698 KAPILLALVA708 GEAAGIMENI718 SDDVIVGRCL728 AILKGIFGSS 738 AVPQPKETVV748 SRWRADPWAR758 GSYSYVAAGS768 SGNDYDLMAQ778 PITPGPPIPR 795 LFFAGEHTIR805 NYPATVHGAL815 LSGLREAGRI825 ADQFLGA
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| PDB ID: 6KGP LSD1-S2157 N5 adduct model | ||||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [1] |
| PDB Sequence |
SGVEGAAFQS
181 RLPHDRMTSQ191 EAACFPDIIS201 GPQQTQKVFL211 FIRNRTLQLW221 LDNPKIQLTF 231 EATLQQLEAP241 YNSDTVLVHR251 VHSYLERHGL261 INFGIYKRIK271 PLPTKKTGKV 281 IIIGSGVSGL291 AAARQLQSFG301 MDVTLLEARD311 RVGGRVATFR321 KGNYVADLGA 331 MVVTGLGGNP341 MAVVSKQVNM351 ELAKIKQKCP361 LYEANGQAVP371 KEKDEMVEQE 381 FNRLLEATSY391 LSHQLDFNVL401 NNKPVSLGQA411 LEVVIQLQEK421 HVKDEQIEHW 431 KKIVKTQEEL441 KELLNKMVNL451 KEKIKELHQQ461 YKEADITAEF478 LVKSKHRDLT 488 ALCKEYDELA498 ETQGKLEEKL508 QELEANPPSD518 VYLSSRDRQI528 LDWHFANLEF 538 ANATPLSTLS548 LKHWDQDDDF558 EFTGSHLTVR568 NGYSCVPVAL578 AEGLDIKLNT 588 AVRQVRYTAS598 GCEVIAVNTR608 STSQTFIYKC618 DAVLCTLPLG628 VLKQQPPAVQ 638 FVPPLPEWKT648 SAVQRMGFGN658 LNKVVLCFDR668 VFWDPSVNLF678 GHVGSTTASR 688 GELFLFWNLY698 KAPILLALVA708 GEAAGIMENI718 SDDVIVGRCL728 AILKGIFGSS 738 AVPQPKETVV748 SRWRADPWAR758 GSYSYVAAGS768 SGNDYDLMAQ778 PITPGPPIPR 795 LFFAGEHTIR805 NYPATVHGAL815 LSGLREAGRI825 ADQFLGA
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| PDB ID: 6KGM LSD1-CoREST-S2116 five-membered ring adduct model | ||||||
| Method | X-ray diffraction | Resolution | 2.62 Å | Mutation | No | [1] |
| PDB Sequence |
SGVEGAAFQS
181 RLPHDRMTSQ191 EAACFPDIIS201 GPQQTQKVFL211 FIRNRTLQLW221 LDNPKIQLTF 231 EATLQQLEAP241 YNSDTVLVHR251 VHSYLERHGL261 INFGIYKRIK271 PLPTKKTGKV 281 IIIGSGVSGL291 AAARQLQSFG301 MDVTLLEARD311 RVGGRVATFR321 KGNYVADLGA 331 MVVTGLGGNP341 MAVVSKQVNM351 ELAKIKQKCP361 LYEANGQAVP371 KEKDEMVEQE 381 FNRLLEATSY391 LSHQLDFNVL401 NNKPVSLGQA411 LEVVIQLQEK421 HVKDEQIEHW 431 KKIVKTQEEL441 KELLNKMVNL451 KEKIKELHQQ461 YKEASEVKPP471 RDITAEFLVK 481 SKHRDLTALC491 KEYDELAETQ501 GKLEEKLQEL511 EANPPSDVYL521 SSRDRQILDW 531 HFANLEFANA541 TPLSTLSLKH551 WDQDDDFEFT561 GSHLTVRNGY571 SCVPVALAEG 581 LDIKLNTAVR591 QVRYTASGCE601 VIAVNTRSTS611 QTFIYKCDAV621 LCTLPLGVLK 631 QQPPAVQFVP641 PLPEWKTSAV651 QRMGFGNLNK661 VVLCFDRVFW671 DPSVNLFGHV 681 GSTTASRGEL691 FLFWNLYKAP701 ILLALVAGEA711 AGIMENISDD721 VIVGRCLAIL 731 KGIFGSSAVP741 QPKETVVSRW751 RADPWARGSY761 SYVAAGSSGN771 DYDLMAQPIT 781 PGPSIPGAPQ791 PIPRLFFAGE801 HTIRNYPATV811 HGALLSGLRE821 AGRIADQFLG 831 A
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| PDB ID: 6KGN LSD1-CoREST-S2116 N5 adduct model | ||||||
| Method | X-ray diffraction | Resolution | 2.62 Å | Mutation | No | [1] |
| PDB Sequence |
SGVEGAAFQS
181 RLPHDRMTSQ191 EAACFPDIIS201 GPQQTQKVFL211 FIRNRTLQLW221 LDNPKIQLTF 231 EATLQQLEAP241 YNSDTVLVHR251 VHSYLERHGL261 INFGIYKRIK271 PLPTKKTGKV 281 IIIGSGVSGL291 AAARQLQSFG301 MDVTLLEARD311 RVGGRVATFR321 KGNYVADLGA 331 MVVTGLGGNP341 MAVVSKQVNM351 ELAKIKQKCP361 LYEANGQAVP371 KEKDEMVEQE 381 FNRLLEATSY391 LSHQLDFNVL401 NNKPVSLGQA411 LEVVIQLQEK421 HVKDEQIEHW 431 KKIVKTQEEL441 KELLNKMVNL451 KEKIKELHQQ461 YKEASEVKPP471 RDITAEFLVK 481 SKHRDLTALC491 KEYDELAETQ501 GKLEEKLQEL511 EANPPSDVYL521 SSRDRQILDW 531 HFANLEFANA541 TPLSTLSLKH551 WDQDDDFEFT561 GSHLTVRNGY571 SCVPVALAEG 581 LDIKLNTAVR591 QVRYTASGCE601 VIAVNTRSTS611 QTFIYKCDAV621 LCTLPLGVLK 631 QQPPAVQFVP641 PLPEWKTSAV651 QRMGFGNLNK661 VVLCFDRVFW671 DPSVNLFGHV 681 GSTTASRGEL691 FLFWNLYKAP701 ILLALVAGEA711 AGIMENISDD721 VIVGRCLAIL 731 KGIFGSSAVP741 QPKETVVSRW751 RADPWARGSY761 SYVAAGSSGN771 DYDLMAQPIT 781 PGPSIPGAPQ791 PIPRLFFAGE801 HTIRNYPATV811 HGALLSGLRE821 AGRIADQFLG 831 A
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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 .DJ0 or .DJ02 or .DJ03 or :3DJ0;style chemicals stick;color identity;select .A:330 or .A:331 or .A:332 or .A:333 or .A:335 or .A:538 or .A:539 or .A:564 or .A:659 or .A:661 or .A:761 or .A:808 or .A:809 or .A:810; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 6KGK LSD1-CoREST-S2101 five-membered ring adduct model | ||||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [1] |
| PDB Sequence |
SGVEGAAFQS
181 RLPHDRMTSQ191 EAACFPDIIS201 GPQQTQKVFL211 FIRNRTLQLW221 LDNPKIQLTF 231 EATLQQLEAP241 YNSDTVLVHR251 VHSYLERHGL261 INFGIYKRIK271 PLPTKKTGKV 281 IIIGSGVSGL291 AAARQLQSFG301 MDVTLLEARD311 RVGGRVATFR321 KGNYVADLGA 331 MVVTGLGGNP341 MAVVSKQVNM351 ELAKIKQKCP361 LYEANGQAVP371 KEKDEMVEQE 381 FNRLLEATSY391 LSHQLDFNVL401 NNKPVSLGQA411 LEVVIQLQEK421 HVKDEQIEHW 431 KKIVKTQEEL441 KELLNKMVNL451 KEKIKELHQQ461 YKEASEVKPP471 RDITAEFLVK 481 SKHRDLTALC491 KEYDELAETQ501 GKLEEKLQEL511 EANPPSDVYL521 SSRDRQILDW 531 HFANLEFANA541 TPLSTLSLKH551 WDQDDDFEFT561 GSHLTVRNGY571 SCVPVALAEG 581 LDIKLNTAVR591 QVRYTASGCE601 VIAVNTRSTS611 QTFIYKCDAV621 LCTLPLGVLK 631 QQPPAVQFVP641 PLPEWKTSAV651 QRMGFGNLNK661 VVLCFDRVFW671 DPSVNLFGHV 681 GSTTASRGEL691 FLFWNLYKAP701 ILLALVAGEA711 AGIMENISDD721 VIVGRCLAIL 731 KGIFGSSAVP741 QPKETVVSRW751 RADPWARGSY761 SYVAAGSSGN771 DYDLMAQPIT 781 PGPSIPGAPQ791 PIPRLFFAGE801 HTIRNYPATV811 HGALLSGLRE821 AGRIADQFLG 831 A
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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 .DJ0 or .DJ02 or .DJ03 or :3DJ0;style chemicals stick;color identity;select .A:330 or .A:331 or .A:332 or .A:333 or .A:335 or .A:538 or .A:539 or .A:564 or .A:659 or .A:661 or .A:761 or .A:808 or .A:809 or .A:810; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 6KGL LSD1-CoREST-S2101 N5 adduct model | ||||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [1] |
| PDB Sequence |
SGVEGAAFQS
181 RLPHDRMTSQ191 EAACFPDIIS201 GPQQTQKVFL211 FIRNRTLQLW221 LDNPKIQLTF 231 EATLQQLEAP241 YNSDTVLVHR251 VHSYLERHGL261 INFGIYKRIK271 PLPTKKTGKV 281 IIIGSGVSGL291 AAARQLQSFG301 MDVTLLEARD311 RVGGRVATFR321 KGNYVADLGA 331 MVVTGLGGNP341 MAVVSKQVNM351 ELAKIKQKCP361 LYEANGQAVP371 KEKDEMVEQE 381 FNRLLEATSY391 LSHQLDFNVL401 NNKPVSLGQA411 LEVVIQLQEK421 HVKDEQIEHW 431 KKIVKTQEEL441 KELLNKMVNL451 KEKIKELHQQ461 YKEASEVKPP471 RDITAEFLVK 481 SKHRDLTALC491 KEYDELAETQ501 GKLEEKLQEL511 EANPPSDVYL521 SSRDRQILDW 531 HFANLEFANA541 TPLSTLSLKH551 WDQDDDFEFT561 GSHLTVRNGY571 SCVPVALAEG 581 LDIKLNTAVR591 QVRYTASGCE601 VIAVNTRSTS611 QTFIYKCDAV621 LCTLPLGVLK 631 QQPPAVQFVP641 PLPEWKTSAV651 QRMGFGNLNK661 VVLCFDRVFW671 DPSVNLFGHV 681 GSTTASRGEL691 FLFWNLYKAP701 ILLALVAGEA711 AGIMENISDD721 VIVGRCLAIL 731 KGIFGSSAVP741 QPKETVVSRW751 RADPWARGSY761 SYVAAGSSGN771 DYDLMAQPIT 781 PGPSIPGAPQ791 PIPRLFFAGE801 HTIRNYPATV811 HGALLSGLRE821 AGRIADQFLG 831 A
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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 .DJ0 or .DJ02 or .DJ03 or :3DJ0;style chemicals stick;color identity;select .A:330 or .A:331 or .A:332 or .A:333 or .A:335 or .A:538 or .A:539 or .A:564 or .A:659 or .A:661 or .A:761 or .A:808 or .A:809 or .A:810; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. ChemMedChem. 2020 May 6;15(9):787-793. | ||||
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