Structure of PDB 7jvu Chain B Binding Site BS03

Receptor Information
>7jvu Chain B (length=362) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPVYIYSPEYVSMCDSLAKIPKRASMVHSLTEAYALHKQMRIVKPKVASM
EEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAA
IGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILR
LRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDV
SDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQL
GADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARC
WTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQ
ILNYIKGNLKHV
Ligand information
Ligand IDSHH
InChIInChI=1S/C14H20N2O3/c17-13(15-12-8-4-3-5-9-12)10-6-1-2-7-11-14(18)16-19/h3-5,8-9,19H,1-2,6-7,10-11H2,(H,15,17)(H,16,18)
InChIKeyWAEXFXRVDQXREF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341ONC(=O)CCCCCCC(=O)Nc1ccccc1
OpenEye OEToolkits 1.5.0c1ccc(cc1)NC(=O)CCCCCCC(=O)NO
ACDLabs 10.04O=C(Nc1ccccc1)CCCCCCC(=O)NO
FormulaC14 H20 N2 O3
NameOCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE;
SAHA
ChEMBLCHEMBL98
DrugBankDB02546
ZINCZINC000001543873
PDB chain7jvu Chain B Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7jvu Structural analysis of histone deacetylase 8 mutants associated with Cornelia de Lange Syndrome spectrum disorders.
Resolution1.50048 Å
Binding residue
(original residue number in PDB)		H142 H143 G151 F152 D178 H180 F208 Y306
Binding residue
(residue number reindexed from 1)		H128 H129 G137 F138 D164 H166 F194 Y292
Annotation score1
Binding affinityBindingDB: IC50=2000nM,Ki=480nM,Kd=1.2e+3nM
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0030544 Hsp70 protein binding
GO:0033558 protein lysine deacetylase activity
GO:0046872 metal ion binding
GO:0051879 Hsp90 protein binding
GO:0140297 DNA-binding transcription factor binding
GO:0160008 protein decrotonylase activity
GO:0160009 histone decrotonylase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0007064 mitotic sister chromatid cohesion
GO:0031397 negative regulation of protein ubiquitination
GO:0031647 regulation of protein stability
GO:0032204 regulation of telomere maintenance
GO:0040029 epigenetic regulation of gene expression
Cellular Component
GO:0000118 histone deacetylase complex
GO:0000228 nuclear chromosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7jvu, PDBe:7jvu, PDBj:7jvu
PDBsum7jvu
PubMed33316326
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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