Structure of PDB 7xw8 Chain A Binding Site BS01

Receptor Information
>7xw8 Chain A (length=639) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV
PKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHITAEFLVKSKH
RDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFA
NLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDI
KLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQP
PAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGST
TASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGI
FGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPQP
IPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLG
Ligand information
Ligand IDFA8
InChIInChI=1S/C27H35N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,18-21,26,32,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,18-,19-,20+,21+,26+/m0/s1
InChIKeySDBHOOIZTSVSKT-LDVRFEIFSA-N
SMILES
SoftwareSMILES
CACTVS 3.352Cc1cc2N[CH]3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.6.1Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.352Cc1cc2N[C@@H]3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.6.1Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@H]3N2)C[C@@H]([C@@H]([C@@H](CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
ACDLabs 10.04O=C2NC(=O)N=C3N(c1cc(c(cc1NC23)C)C)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O
FormulaC27 H35 N9 O15 P2
Name
ChEMBL
DrugBank
ZINCZINC000098208864
PDB chain7xw8 Chain A Residue 904 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7xw8 Design, synthesis, and structure-activity relationship of TAK-418 and its derivatives as a novel series of LSD1 inhibitors with lowered risk of hematological side effects.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		G285 G287 S289 L307 E308 A309 R310 G315 R316 G330 A331 M332 V333 V590 L625 P626 W751 W756 S760 Y761 G800 E801 T810 V811 A814
Binding residue
(residue number reindexed from 1)		G115 G117 S119 L137 E138 A139 R140 G145 R146 G160 A161 M162 V163 V406 L441 P442 W567 W572 S576 Y577 G608 E609 T618 V619 A622
Annotation score1
Enzymatic activity
Enzyme Commision number 1.14.99.66: [histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7xw8, PDBe:7xw8, PDBj:7xw8
PDBsum7xw8
PubMed35749987
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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