Structure of PDB 7jvu Chain A Binding Site BS03

Receptor Information
>7jvu Chain A (length=365) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLTEAYALHKQMRIVKPKVAS
MEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAA
AIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGIL
RLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGD
VSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQ
LGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTAR
CWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQ
QILNYIKGNLKHVVI
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)		P273 M274 Y306
Binding residue
(residue number reindexed from 1)		P260 M261 Y293
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

View graph for
Molecular Function
View graph for
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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