Structure of PDB 6oda Chain C Binding Site BS01

Receptor Information
>6oda Chain C (length=353) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVAS
MEEMATFHTDAYLQHLQKVSQEYGLGYDCPATEGIFDYAAAIGGATITAA
QCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERIL
YVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGR
YYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDP
MCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVIL
GKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNL
KHV
Ligand information
Ligand IDC7
InChIInChI=1S/C17H15F3N2O3/c18-17(19,20)13-6-3-5-12(10-13)16(24)21-14-7-2-1-4-11(14)8-9-15(23)22-25/h1-7,10,25H,8-9H2,(H,21,24)(H,22,23)
InChIKeyQXXNUWFIASXMCG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(c(c1)CCC(=O)NO)NC(=O)c2cccc(c2)C(F)(F)F
CACTVS 3.385ONC(=O)CCc1ccccc1NC(=O)c2cccc(c2)C(F)(F)F
ACDLabs 12.01O=C(NO)CCc1c(cccc1)NC(c2cc(ccc2)C(F)(F)F)=O
FormulaC17 H15 F3 N2 O3
NameN-{2-[3-(hydroxyamino)-3-oxopropyl]phenyl}-3-(trifluoromethyl)benzamide
ChEMBL
DrugBank
ZINC
PDB chain6oda Chain C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6oda Structure-based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-oxoimidazolidin-1-yl)phenyl)acrylamides as Potent and Selective HDAC8 inhibitors
Resolution2.88 Å
Binding residue
(original residue number in PDB)		H142 H143 G151 D178 H180 F208 M274 Y306
Binding residue
(residue number reindexed from 1)		H119 H120 G128 D155 H157 F185 M251 Y283
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
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Cellular Component
External links
PDB RCSB:6oda, PDBe:6oda, PDBj:6oda
PDBsum6oda
PubMed
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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