Structure of PDB 7m40 Chain A Binding Site BS01

Receptor Information
>7m40 Chain A (length=401) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPE
GKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGG
FGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKH
PSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDI
SAVPKGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTR
SNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKL
KLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPDA
EDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIY
N
Ligand information
Ligand IDYQJ
InChIInChI=1S/C21H34N6O2/c1-25(2)10-7-9-22-21-23-17-13-19(29-6)18(28-5)12-16(17)20(24-21)27-11-8-15(14-27)26(3)4/h12-13,15H,7-11,14H2,1-6H3,(H,22,23,24)
InChIKeyYLRHAJMWBVABHS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN(C)CCCNc1nc2cc(c(cc2c(n1)N3CCC(C3)N(C)C)OC)OC
ACDLabs 12.01CN(C)CCCNc1nc2cc(OC)c(OC)cc2c(n1)N1CCC(C1)N(C)C
CACTVS 3.385COc1cc2nc(NCCCN(C)C)nc(N3CCC(C3)N(C)C)c2cc1OC
FormulaC21 H34 N6 O2
NameN~3~-{4-[3-(dimethylamino)pyrrolidin-1-yl]-6,7-dimethoxyquinazolin-2-yl}-N~1~,N~1~-dimethylpropane-1,3-diamine
ChEMBL
DrugBank
ZINC
PDB chain7m40 Chain A Residue 1000 [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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PDB7m40 Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4)
Resolution1.88 Å
Binding residue
(original residue number in PDB)		R129 Y181 E231 E319 F321
Binding residue
(residue number reindexed from 1)		R122 Y174 E223 E311 F313
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0005515 protein binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0031492 nucleosomal DNA binding
GO:0042393 histone binding
GO:0042826 histone deacetylase binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006260 DNA replication
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0006335 DNA replication-dependent chromatin assembly
GO:0006338 chromatin remodeling
GO:0006355 regulation of DNA-templated transcription
GO:0007420 brain development
GO:0008285 negative regulation of cell population proliferation
GO:0030336 negative regulation of cell migration
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0042659 regulation of cell fate specification
GO:0045892 negative regulation of DNA-templated transcription
GO:0045893 positive regulation of DNA-templated transcription
GO:1902455 negative regulation of stem cell population maintenance
GO:1902459 positive regulation of stem cell population maintenance
GO:2000736 regulation of stem cell differentiation
Cellular Component
GO:0000118 histone deacetylase complex
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol
GO:0016581 NuRD complex
GO:0016589 NURF complex
GO:0032991 protein-containing complex
GO:0033186 CAF-1 complex
GO:0035098 ESC/E(Z) complex
GO:0070822 Sin3-type complex
GO:1904949 ATPase complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7m40, PDBe:7m40, PDBj:7m40
PDBsum7m40
PubMed
UniProtQ09028|RBBP4_HUMAN Histone-binding protein RBBP4 (Gene Name=RBBP4)

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