Structure of PDB 3f0r Chain B Binding Site BS02

Receptor Information
>3f0r Chain B (length=366) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVA
SMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYA
AAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGI
LRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTG
DVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVL
QLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTA
RCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRI
QQILNYIKGNLKHVVI
Ligand information
Ligand IDTSN
InChIInChI=1S/C17H22N2O3/c1-12(5-10-16(20)18-22)11-13(2)17(21)14-6-8-15(9-7-14)19(3)4/h5-11,13,22H,1-4H3,(H,18,20)/b10-5+,12-11+/t13-/m1/s1
InChIKeyRTKIYFITIVXBLE-QEQCGCAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH](C=C(C)C=CC(=O)NO)C(=O)c1ccc(cc1)N(C)C
CACTVS 3.341C[C@H](\C=C(C)\C=C\C(=O)NO)C(=O)c1ccc(cc1)N(C)C
ACDLabs 10.04O=C(NO)\C=C\C(=C\C(C(=O)c1ccc(N(C)C)cc1)C)C
OpenEye OEToolkits 1.5.0CC(C=C(C)C=CC(=O)NO)C(=O)c1ccc(cc1)N(C)C
OpenEye OEToolkits 1.5.0C[C@H](\C=C(/C)\C=C\C(=O)NO)C(=O)c1ccc(cc1)N(C)C
FormulaC17 H22 N2 O3
NameTRICHOSTATIN A;
7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE
ChEMBLCHEMBL99
DrugBankDB04297
ZINCZINC000100014731
PDB chain3f0r Chain B Residue 804 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3f0r Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors.
Resolution2.54 Å
Binding residue
(original residue number in PDB)		Y100 H143 F152 D178 H180 M274 Y306
Binding residue
(residue number reindexed from 1)		Y88 H131 F140 D166 H168 M262 Y294
Annotation score1
Binding affinityBindingDB: IC50=90nM,Ki=45nM,Kd=3.9e+2nM
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:3f0r, PDBe:3f0r, PDBj:3f0r
PDBsum3f0r
PubMed19053282
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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