Structure of PDB 2v5x Chain B Binding Site BS03

Receptor Information
>2v5x Chain B (length=356) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVAS
MEEMATFHTDAYLQHLQKVSQEGIEYGLGYDCPATEGIFDYAAAIGGATI
TAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFE
RILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLG
KGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIA
GDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTG
VILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIK
GNLKHV
Ligand information
Ligand IDV5X
InChIInChI=1S/C36H41N5O5/c1-23-28(29-21-25(46-2)17-18-31(29)38-23)22-34(43)39-32(15-7-4-8-16-33(42)41-45)36(44)37-20-19-27-26-13-9-10-14-30(26)40-35(27)24-11-5-3-6-12-24/h3,5-6,9-14,17-18,21,32,38,40,45H,4,7-8,15-16,19-20,22H2,1-2H3,(H,37,44)(H,39,43)(H,41,42)/t32-/m1/s1
InChIKeyVBWCMILVHANAGG-JGCGQSQUSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NCCc3c1ccccc1nc3c2ccccc2)C(NC(=O)Cc5c4cc(OC)ccc4nc5C)CCCCCC(=O)NO
OpenEye OEToolkits 1.5.0Cc1c(c2cc(ccc2[nH]1)OC)CC(=O)NC(CCCCCC(=O)NO)C(=O)NCCc3c4ccccc4[nH]c3c5ccccc5
CACTVS 3.341COc1ccc2[nH]c(C)c(CC(=O)N[C@H](CCCCCC(=O)NO)C(=O)NCCc3c([nH]c4ccccc34)c5ccccc5)c2c1
CACTVS 3.341COc1ccc2[nH]c(C)c(CC(=O)N[CH](CCCCCC(=O)NO)C(=O)NCCc3c([nH]c4ccccc34)c5ccccc5)c2c1
OpenEye OEToolkits 1.5.0Cc1c(c2cc(ccc2[nH]1)OC)CC(=O)N[C@H](CCCCCC(=O)NO)C(=O)NCCc3c4ccccc4[nH]c3c5ccccc5
FormulaC36 H41 N5 O5
Name(2R)-N~8~-HYDROXY-2-{[(5-METHOXY-2-METHYL-1H-INDOL-3-YL)ACETYL]AMINO}-N~1~-[2-(2-PHENYL-1H-INDOL-3-YL)ETHYL]OCTANEDIAMIDE
ChEMBL
DrugBank
ZINCZINC000016052583
PDB chain2v5x Chain B Residue 1380 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2v5x Substrate Binding to Histone Deacetylases as Revealed by Crystal Structure of Hdac8-Substrate Complex
Resolution2.25 Å
Binding residue
(original residue number in PDB)		D101 H142 H143 F152 D178 H180 F208 P209 G210 Y306
Binding residue
(residue number reindexed from 1)		D81 H122 H123 F132 D158 H160 F188 P189 G190 Y286
Annotation score1
Binding affinityMOAD: Kd=220nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2v5x, PDBe:2v5x, PDBj:2v5x
PDBsum2v5x
PubMed17721440
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

[Back to BioLiP]