Structure of PDB 5yjb Chain A Binding Site BS02

Receptor Information
>5yjb Chain A (length=661) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLW
LDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIK
PLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFR
KGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVP
KEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEK
HVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPP
RDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYL
SSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGY
SCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAV
LCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFW
DPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDD
VIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGN
DYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLRE
AGRIADQFLGA
Ligand information
Ligand ID8WC
InChIInChI=1S/C25H25N3O/c1-18-2-6-22(7-3-18)25-24(21-8-4-19(15-26)5-9-21)14-23(16-28-25)29-17-20-10-12-27-13-11-20/h2-9,14,16,20,27H,10-13,17H2,1H3
InChIKeyJQPWKVGXPWCDEE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(cc1)c2ncc(OCC3CCNCC3)cc2c4ccc(cc4)C#N
OpenEye OEToolkits 2.0.6Cc1ccc(cc1)c2c(cc(cn2)OCC3CCNCC3)c4ccc(cc4)C#N
FormulaC25 H25 N3 O
Name4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile
ChEMBLCHEMBL3759201
DrugBank
ZINCZINC000653703179
PDB chain5yjb Chain A Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yjb Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile.
Resolution2.96 Å
Binding residue
(original residue number in PDB)		M332 F538 D555 L659 K661 W695 A809
Binding residue
(residue number reindexed from 1)		M161 F367 D384 L488 K490 W524 A638
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.54,Ki=29nM
BindingDB: Ki=29nM
Enzymatic activity
Catalytic site (original residue number in PDB) T335 D553 K661
Catalytic site (residue number reindexed from 1) T164 D382 K490
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:5yjb, PDBe:5yjb, PDBj:5yjb
PDBsum5yjb
PubMed29949906
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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