Structure of PDB 7xw8 Chain A Binding Site BS02

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 IDI00
InChIInChI=1S/C13H17NO3S/c15-5-1-2-12-8-10(9-18-12)13(16)14-11-3-6-17-7-4-11/h5,8-9,11H,1-4,6-7H2,(H,14,16)
InChIKeyAYXNENHDYPBMFV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=CCCc1scc(c1)C(=O)NC2CCOCC2
OpenEye OEToolkits 2.0.7c1c(csc1CCC=O)C(=O)NC2CCOCC2
FormulaC13 H17 N O3 S
Name~{N}-(oxan-4-yl)-5-(3-oxidanylidenepropyl)thiophene-3-carboxamide;
TAK-418 derivertive
ChEMBL
DrugBank
ZINC
PDB chain7xw8 Chain A Residue 905 [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)		F538 W695 Y761 A809
Binding residue
(residue number reindexed from 1)		F354 W511 Y577 A617
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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