Structure of PDB 7kxt Chain B Binding Site BS02

Receptor Information
>7kxt Chain B (length=359) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YSFKCVNSLKEDHNQPLFGVQFNWHSGDPLVFATVGSNRVTLYECHSQGE
IRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQ
CIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGG
VEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYN
PNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCW
KPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGN
QVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDD
ASIWRWDRL
Ligand information
Ligand IDXB7
InChIInChI=1S/C28H31FN4O/c1-34-25-12-8-21(9-13-25)14-17-32-18-15-24(16-19-32)30-28-31-26-4-2-3-5-27(26)33(28)20-22-6-10-23(29)11-7-22/h2-13,24H,14-20H2,1H3,(H,30,31)
InChIKeyGXDALQBWZGODGZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(CCN2CCC(CC2)Nc3nc4ccccc4n3Cc5ccc(F)cc5)cc1
OpenEye OEToolkits 2.0.7COc1ccc(cc1)CCN2CCC(CC2)Nc3nc4ccccc4n3Cc5ccc(cc5)F
ACDLabs 12.01COc1ccc(cc1)CCN2CCC(CC2)Nc4n(c3c(cccc3)n4)Cc5ccc(cc5)F
FormulaC28 H31 F N4 O
Name1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine
ChEMBLCHEMBL296419
DrugBankDB00637
ZINCZINC000000601274
PDB chain7kxt Chain B Residue 501 [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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PDB7kxt Structure-Guided Development of Small-Molecule PRC2 Inhibitors Targeting EZH2-EED Interaction.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		L246 L315 G316 F372 W373 Q374 L391 V393 P396 H397
Binding residue
(residue number reindexed from 1)		L165 L234 G235 F291 W292 Q293 L310 V312 P315 H316
Annotation score1
Binding affinityBindingDB: Ki=23010nM,IC50=93800nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001222 transcription corepressor binding
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0008047 enzyme activator activity
GO:0031491 nucleosome binding
GO:0042802 identical protein binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0021510 spinal cord development
GO:0031507 heterochromatin formation
GO:0045892 negative regulation of DNA-templated transcription
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol
GO:0035098 ESC/E(Z) complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7kxt, PDBe:7kxt, PDBj:7kxt
PDBsum7kxt
PubMed34077206
UniProtO75530|EED_HUMAN Polycomb protein EED (Gene Name=EED)

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