Structure of PDB 6k3e Chain A Binding Site BS01

Receptor Information
>6k3e 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]
GVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWL
DNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKP
LPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRK
GNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPK
EKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKH
VKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPR
DITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLS
SRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYS
CVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVL
CTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWD
PSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDV
IVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGND
YDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREA
GRIADQFLGAM
Ligand information
Ligand IDCW0
InChIInChI=1S/C22H32FN3O2/c23-22(16-25-20-14-19(20)18-4-2-1-3-5-18)8-12-26(13-9-22)21(27)28-15-17-6-10-24-11-7-17/h1-5,17,19-20,24-25H,6-16H2/t19-,20+/m0/s1
InChIKeyCMYNDDNZDLGSJZ-VQTJNVASSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)[C@@H]2C[C@H]2NCC3(CCN(CC3)C(=O)OCC4CCNCC4)F
CACTVS 3.385FC1(CCN(CC1)C(=O)OCC2CCNCC2)CN[C@@H]3C[C@H]3c4ccccc4
OpenEye OEToolkits 2.0.7c1ccc(cc1)C2CC2NCC3(CCN(CC3)C(=O)OCC4CCNCC4)F
CACTVS 3.385FC1(CCN(CC1)C(=O)OCC2CCNCC2)CN[CH]3C[CH]3c4ccccc4
FormulaC22 H32 F N3 O2
Namepiperidin-4-ylmethyl 4-fluoranyl-4-[[[(1~{R},2~{S})-2-phenylcyclopropyl]amino]methyl]piperidine-1-carboxylate
ChEMBL
DrugBank
ZINC
PDB chain6k3e Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6k3e LSD1/Co-Rest structure with an inhibitor
Resolution2.87 Å
Binding residue
(original residue number in PDB)
N535 F538 A539 D555 H564
Binding residue
(residue number reindexed from 1)
N363 F366 A367 D383 H392
Annotation score1
Binding affinityBindingDB: IC50=49.7nM
Enzymatic activity
Catalytic site (original residue number in PDB) T335 D553 K661
Catalytic site (residue number reindexed from 1) T163 D381 K489
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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Cellular Component
External links
PDB RCSB:6k3e, PDBe:6k3e, PDBj:6k3e
PDBsum6k3e
PubMed
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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