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 | [(2r,3s,4r,5r)-5-(6-Amino-9h-Purin-9-Yl)-3,4-Dihydroxytetrahydrofuran-2-Yl]methyl (2r,3s,4s)-5-[7,8-Dimethyl-2,4-Dioxo-5-(3-Phenylpropanoyl)-1,3,4,5-Tetrahydrobenzo[g]pteridin-10(2h)-Yl]-2,3,4-Trihydroxypentyl Dihydrogen Diphosphate | Ligand Info | |||
| Canonical SMILES | CC1=CC2=C(C=C1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=NC6=C(N=CN=C65)N)O)O)O)O)O)NC(=O)NC3=O)C(=O)CCC7=CC=CC=C7 | ||||
| InChI | 1S/C36H43N9O16P2/c1-17-10-20-21(11-18(17)2)45(25(48)9-8-19-6-4-3-5-7-19)27-33(41-36(53)42-34(27)52)43(20)12-22(46)28(49)23(47)13-58-62(54,55)61-63(56,57)59-14-24-29(50)30(51)35(60-24)44-16-40-26-31(37)38-15-39-32(26)44/h3-7,10-11,15-16,22-24,28-30,35,46-47,49-51H,8-9,12-14H2,1-2H3,(H,54,55)(H,56,57)(H2,37,38,39)(H2,41,42,52,53)/t22-,23+,24+,28-,29+,30+,35+/m0/s1 | ||||
| InChIKey | ASOSNULLFLNYFZ-NEHYRMIBSA-N | ||||
| PubChem Compound ID | 23631921 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 2Z3Y Crystal structure of Lysine-specific demethylase1 | ||||||
| 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 YKEDITAEFL479 VKSKHRDLTA 489 LCKEYDELAE499 TQGKLEEKLQ509 ELEANPPSDV519 YLSSRDRQIL529 DWHFANLEFA 539 NATPLSTLSL549 KHWDQDDDFE559 FTGSHLTVRN569 GYSCVPVALA579 EGLDIKLNTA 589 VRQVRYTASG599 CEVIAVNTRS609 TSQTFIYKCD619 AVLCTLPLGV629 LKQQPPAVQF 639 VPPLPEWKTS649 AVQRMGFGNL659 NKVVLCFDRV669 FWDPSVNLFG679 HVGSTTASRG 689 ELFLFWNLYK699 APILLALVAG709 EAAGIMENIS719 DDVIVGRCLA729 ILKGIFGSSA 739 VPQPKETVVS749 RWRADPWARG759 SYSYVAAGSS769 GNDYDLMAQP779 ITPPIPRLFF 798 AGEHTIRNYP808 ATVHGALLSG818 LREAGRIADQ828 FLG
|
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|
|
ILE284
3.988
GLY285
3.207
SER286
3.790
GLY287
3.404
VAL288
3.471
SER289
2.761
GLY290
4.378
LEU307
3.481
GLU308
2.516
ALA309
3.195
ARG310
2.843
GLY314
3.411
GLY315
3.256
ARG316
2.880
VAL317
4.003
LEU329
3.357
GLY330
3.441
ALA331
3.300
MET332
2.944
VAL333
2.774
THR335
3.210
PHE538
3.516
ALA539
4.512
HIS564
4.985
TYR571
4.692
THR588
3.730
ALA589
3.741
VAL590
2.948
ARG591
4.305
THR624
3.411
LEU625
3.420
PRO626
3.486
VAL629
4.286
VAL637
3.929
LEU659
3.523
LYS661
4.210
TRP751
3.515
TRP756
3.296
GLY759
4.751
SER760
3.455
TYR761
3.393
GLY800
3.137
GLU801
2.918
ALA809
3.415
THR810
3.229
VAL811
2.872
HIS812
4.554
ALA814
3.473
|
|||||
| PDB ID: 2EJR LSD1-tranylcypromine complex | ||||||
| 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 YKEDITAEFL479 VKSKHRDLTA 489 LCKEYDELAE499 TQGKLEEKLQ509 ELEANPPSDV519 YLSSRDRQIL529 DWHFANLEFA 539 NATPLSTLSL549 KHWDQDDDFE559 FTGSHLTVRN569 GYSCVPVALA579 EGLDIKLNTA 589 VRQVRYTASG599 CEVIAVNTRS609 TSQTFIYKCD619 AVLCTLPLGV629 LKQQPPAVQF 639 VPPLPEWKTS649 AVQRMGFGNL659 NKVVLCFDRV669 FWDPSVNLFG679 HVGSTTASRG 689 ELFLFWNLYK699 APILLALVAG709 EAAGIMENIS719 DDVIVGRCLA729 ILKGIFGSSA 739 VPQPKETVVS749 RWRADPWARG759 SYSYVAAGSS769 GNDYDLMAQP779 ITPPIPRLFF 798 AGEHTIRNYP808 ATVHGALLSG818 LREAGRIADQ828 FLG
|
|||||
|
|
ILE284
4.141
GLY285
3.248
SER286
3.831
GLY287
3.588
VAL288
3.632
SER289
2.831
GLY290
4.401
LEU307
3.461
GLU308
2.583
ALA309
3.231
ARG310
2.779
GLY314
3.445
GLY315
3.273
ARG316
2.848
VAL317
4.012
LEU329
3.535
GLY330
3.529
ALA331
3.306
MET332
3.046
VAL333
2.783
THR335
3.345
PHE538
3.568
ALA539
4.715
TYR571
4.749
THR588
3.673
ALA589
3.692
VAL590
2.953
ARG591
4.315
THR624
3.378
LEU625
3.495
PRO626
3.411
VAL629
4.224
VAL637
3.760
LEU659
3.639
LYS661
4.069
TRP751
3.648
TRP756
3.268
GLY759
4.997
SER760
3.581
TYR761
3.308
GLY800
3.058
GLU801
2.921
ALA809
3.359
THR810
3.120
VAL811
2.685
HIS812
4.385
ALA814
3.557
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A. Biochem Biophys Res Commun. 2008 Feb 1;366(1):15-22. | ||||
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