Structure of PDB 5d1b Chain A Binding Site BS03

Receptor Information
>5d1b Chain A (length=356) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVAS
MEEMATFHTDAYLQHLQKVSQEGEYGLGYDCPATEGIFDYAAAIGEATIT
AAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFER
ILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGK
GRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAG
DPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGV
ILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKG
NLKHVV
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 chain5d1b 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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PDB5d1b Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia de Lange Syndrome Spectrum Disorders.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		M274 Y306
Binding residue
(residue number reindexed from 1)		M253 Y285
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
View graph for
Cellular Component
External links
PDB RCSB:5d1b, PDBe:5d1b, PDBj:5d1b
PDBsum5d1b
PubMed26463496
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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