Structure of PDB 1vkg Chain A Binding Site BS02

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 A 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)		H142 H143 F152 H180 F208 Y306
Binding residue
(residue number reindexed from 1)		H113 H114 F123 H151 F179 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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