Structure of PDB 1vkg Chain A Binding Site BS03

Receptor Information
>1vkg Chain A (length=348) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASM
EEMATFHTDAYLQHLQKVSQEGDDATEGIFDYAAAIGGATITAAQCLIDG
MCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDL
HHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNV
PIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNM
TPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSS
EIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV
Ligand information
Ligand IDCRI
InChIInChI=1S/C24H23N3O4/c1-15-4-6-17(7-5-15)22(28)25-21-13-19(12-20(14-21)24(30)27(2)3)16-8-10-18(11-9-16)23(29)26-31/h4-14,31H,1-3H3,(H,25,28)(H,26,29)
InChIKeyDOPFUKKMSDUVTQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c1ccc(cc1)C)Nc3cc(C(=O)N(C)C)cc(c2ccc(C(=O)NO)cc2)c3
OpenEye OEToolkits 1.5.0Cc1ccc(cc1)C(=O)Nc2cc(cc(c2)C(=O)N(C)C)c3ccc(cc3)C(=O)NO
CACTVS 3.341CN(C)C(=O)c1cc(NC(=O)c2ccc(C)cc2)cc(c1)c3ccc(cc3)C(=O)NO
FormulaC24 H23 N3 O4
Name5-(4-METHYL-BENZOYLAMINO)-BIPHENYL-3,4'-DICARBOXYLIC ACID 3-DIMETHYLAMIDE-4'-HYDROXYAMIDE
ChEMBL
DrugBankDB07586
ZINCZINC000016051592
PDB chain1vkg Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1vkg Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases
Resolution2.2 Å
Binding residue
(original residue number in PDB)		P273 M274 Y306
Binding residue
(residue number reindexed from 1)		P244 M245 Y277
Annotation score1
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:1vkg, PDBe:1vkg, PDBj:1vkg
PDBsum1vkg
PubMed15242608
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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