Structure of PDB 6w4k Chain A Binding Site BS01

Receptor Information
>6w4k Chain A (length=651) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLD
NPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPL
PTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKG
NYVADLGAMVVTGLGGNPMMELAKIKQKCPLYEANGQAVPKEKDEMVEQE
FNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHW
KKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVK
SKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDW
HFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEG
LDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLK
QQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHV
GSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAIL
KGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPIT
PGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLG
A
Ligand information
Ligand IDV0Y
InChIInChI=1S/C24H23F2N5O2/c1-30-23(32)21(14-5-6-20(33-2)19(26)11-14)22(15-3-4-16(13-27)18(25)12-15)29-24(30)31-9-7-17(28)8-10-31/h3-6,11-12,17H,7-10,28H2,1-2H3
InChIKeyNBAIXBAUHIQQGF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN1C(=O)C(=C(N=C1N2CCC(CC2)N)c3ccc(c(c3)F)C#N)c4ccc(c(c4)F)OC
CACTVS 3.385COc1ccc(cc1F)C2=C(N=C(N(C)C2=O)N3CCC(N)CC3)c4ccc(C#N)c(F)c4
ACDLabs 12.01N#Cc1c(cc(cc1)C=3N=C(N2CCC(N)CC2)N(C(C=3c4cc(F)c(OC)cc4)=O)C)F
FormulaC24 H23 F2 N5 O2
Name4-[2-(4-aminopiperidin-1-yl)-5-(3-fluoro-4-methoxyphenyl)-1-methyl-6-oxo-1,6-dihydropyrimidin-4-yl]-2-fluorobenzonitrile
ChEMBLCHEMBL4651180
DrugBank
ZINC
PDB chain6w4k Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6w4k Discovery of CC-90011: A Potent and Selective Reversible Inhibitor of Lysine Specific Demethylase 1 (LSD1).
Resolution2.93 Å
Binding residue
(original residue number in PDB)		M332 V333 I356 Q358 F538 A539 D555 H564 K661 W695 Y761 A809
Binding residue
(residue number reindexed from 1)		M159 V160 I175 Q177 F357 A358 D374 H383 K480 W514 Y580 A628
Annotation score1
Binding affinityBindingDB: IC50=<100nM
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

View graph for
Molecular Function
External links
PDB RCSB:6w4k, PDBe:6w4k, PDBj:6w4k
PDBsum6w4k
PubMed33034194
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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