Structure of PDB 8a0b Chain A Binding Site BS01

Receptor Information
>8a0b Chain A (length=369) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYR
PHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDG
LFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVND
IVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYF
PGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPS
AVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTI
RNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNT
PEYMEKIKQRLFENLRMLP
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain8a0b Chain A Residue 601 [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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PDB8a0b Fragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor.
Resolution1.746 Å
Binding residue
(original residue number in PDB)		D181 H183 D269
Binding residue
(residue number reindexed from 1)		D171 H173 D259
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0019213 deacetylase activity
GO:0019899 enzyme binding
GO:0031072 heat shock protein binding
GO:0031492 nucleosomal DNA binding
GO:0033558 protein lysine deacetylase activity
GO:0042393 histone binding
GO:0042826 histone deacetylase binding
GO:0051059 NF-kappaB binding
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
GO:0140297 DNA-binding transcription factor binding
GO:0160008 protein decrotonylase activity
GO:0160009 histone decrotonylase activity
GO:0160010 protein de-2-hydroxyisobutyrylase activity
GO:1990841 promoter-specific chromatin binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001975 response to amphetamine
GO:0003300 cardiac muscle hypertrophy
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0008284 positive regulation of cell population proliferation
GO:0009410 response to xenobiotic stimulus
GO:0009913 epidermal cell differentiation
GO:0010718 positive regulation of epithelial to mesenchymal transition
GO:0010944 negative regulation of transcription by competitive promoter binding
GO:0010977 negative regulation of neuron projection development
GO:0016358 dendrite development
GO:0030336 negative regulation of cell migration
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0031000 response to caffeine
GO:0031507 heterochromatin formation
GO:0032496 response to lipopolysaccharide
GO:0032732 positive regulation of interleukin-1 production
GO:0032760 positive regulation of tumor necrosis factor production
GO:0032922 circadian regulation of gene expression
GO:0032967 positive regulation of collagen biosynthetic process
GO:0034605 cellular response to heat
GO:0035094 response to nicotine
GO:0036211 protein modification process
GO:0042220 response to cocaine
GO:0042475 odontogenesis of dentin-containing tooth
GO:0042659 regulation of cell fate specification
GO:0042733 embryonic digit morphogenesis
GO:0043066 negative regulation of apoptotic process
GO:0043433 negative regulation of DNA-binding transcription factor activity
GO:0045347 negative regulation of MHC class II biosynthetic process
GO:0045862 positive regulation of proteolysis
GO:0045892 negative regulation of DNA-templated transcription
GO:0045893 positive regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048149 behavioral response to ethanol
GO:0048511 rhythmic process
GO:0048714 positive regulation of oligodendrocyte differentiation
GO:0055093 response to hyperoxia
GO:0060789 hair follicle placode formation
GO:0061000 negative regulation of dendritic spine development
GO:0061029 eyelid development in camera-type eye
GO:0061198 fungiform papilla formation
GO:0070301 cellular response to hydrogen peroxide
GO:0071300 cellular response to retinoic acid
GO:0071560 cellular response to transforming growth factor beta stimulus
GO:0097305 response to alcohol
GO:1902437 positive regulation of male mating behavior
GO:1902455 negative regulation of stem cell population maintenance
GO:1902459 positive regulation of stem cell population maintenance
GO:1903351 cellular response to dopamine
GO:1904645 response to amyloid-beta
GO:2000273 positive regulation of signaling receptor activity
GO:2000736 regulation of stem cell differentiation
GO:2000757 negative regulation of peptidyl-lysine acetylation
Cellular Component
GO:0000118 histone deacetylase complex
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016581 NuRD complex
GO:0032991 protein-containing complex
GO:0035098 ESC/E(Z) complex
GO:0070822 Sin3-type complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8a0b, PDBe:8a0b, PDBj:8a0b
PDBsum8a0b
PubMed36262388
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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