Structure of PDB 5dc5 Chain A Binding Site BS01

Receptor Information
>5dc5 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]
LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVAS
MEEMATFHTDAYLQHLQKVSQDDDHPDSIEYGLGYDCPATEGIFDYAAAI
GGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRL
RRKFERILYVNLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVS
DVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLG
ADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCW
TYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQI
LNYIKGNLKHVVIE
Ligand information
Ligand IDB3N
InChIInChI=1S/C16H25N3O3/c1-19(2)14-10-8-13(9-11-14)16(21)17-12-6-4-3-5-7-15(20)18-22/h8-11,22H,3-7,12H2,1-2H3,(H,17,21)(H,18,20)
InChIKeyMXWDSZWTBOCWBK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NO)CCCCCCNC(=O)c1ccc(N(C)C)cc1
CACTVS 3.370
OpenEye OEToolkits 1.7.0		CN(C)c1ccc(cc1)C(=O)NCCCCCCC(=O)NO
FormulaC16 H25 N3 O3
Name4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide;
M344
ChEMBLCHEMBL140000
DrugBankDB02565
ZINCZINC000012502280
PDB chain5dc5 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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PDB5dc5 General Base-General Acid Catalysis in Human Histone Deacetylase 8.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		Y100 H142 H143 G151 F152 D178 H180 F208 Y306
Binding residue
(residue number reindexed from 1)		Y85 H127 H128 G136 F137 D163 H165 F193 Y291
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:5dc5, PDBe:5dc5, PDBj:5dc5
PDBsum5dc5
PubMed26806311
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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