Structure of PDB 5fcw Chain A Binding Site BS01

Receptor Information
>5fcw Chain A (length=364) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVA
SMEEMATFHTDAYLQHLQKVSQEGDDHPDSIEYGLGYDCPATEGIFDYAA
AIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGIL
RLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGD
VSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQ
LGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTAR
CWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQ
QILNYIKGNLKHVV
Ligand information
Ligand ID5YA
InChIInChI=1S/C17H13NO2/c19-17(18-20)14-10-8-13(9-11-14)16-7-3-5-12-4-1-2-6-15(12)16/h1-11,20H,(H,18,19)
InChIKeyPKQVYJOPUCLLCD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1ccc2c(c1)cccc2c3ccc(cc3)C(=O)NO
CACTVS 3.385ONC(=O)c1ccc(cc1)c2cccc3ccccc23
FormulaC17 H13 N O2
Name4-naphthalen-1-yl-~{N}-oxidanyl-benzamide
ChEMBLCHEMBL156887
DrugBank
ZINCZINC000027646659
PDB chain5fcw Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5fcw Structure of 'linkerless' hydroxamic acid inhibitor-HDAC8 complex confirms the formation of an isoform-specific subpocket.
Resolution1.979 Å
Binding residue
(original residue number in PDB)		Y100 D101 H142 H143 D178 H180 F208 Y306
Binding residue
(residue number reindexed from 1)		Y87 D88 H129 H130 D165 H167 F195 Y293
Annotation score1
Binding affinityMOAD: ic50=0.3uM
PDBbind-CN: -logKd/Ki=6.52,IC50=0.3uM
BindingDB: IC50=300nM
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:5fcw, PDBe:5fcw, PDBj:5fcw
PDBsum5fcw
PubMed27374062
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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