Brand  (β version)

PDB ID: 5VI6

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Ligands
Code Name Style Show Link
DIO 1,4-diethylene dioxide PoSSuM
EDO 1,2-ethanediol PoSSuM
K Potassium ion PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
Code Name Show
5OM (2s)-2-amino-8,8-dihydroxy-8-[(2s)-oxiran-2-yl]octanoic acid
CPI 6-carboxypiperidine
Glycosylation
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Modification
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Structure summary

Code : 5VI6   PDBj   RCSB PDB   PDBe
Header : HYDROLASE/HYDROLASE INHIBITOR
Title : Crystal structure of histone deacetylase 8 in complex with trapoxin A
Release Data : 2017-09-06
Compound :
mol_id molecule chains synonym
1 Histone deacetylase 8 A HD8
ec: 3.5.1.98
fragment: residues 8-377
mol_id molecule chains synonym
2 Trapoxin A B (3S,6S,9S,15aR)-6,9-dibenzyl-3-{6,6-dihydroxy-6-[(2S)-oxiran-2-yl]hexyl}octahydro-2H-pyrido[1,2-a][1,4,7,10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: HDAC8, HDACL1, CDA07
mol_id organism_scientific organism_common
2 Helicoma ambiens  (taxid:314151) Ascomycetes
synthetic: yes
Authors : Porter, N.J., Christianson, D.W.
Keywords : HDAC, epigenetics, natural product inhibitor, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 1.237 Å )
Citation :

Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8.

Porter, N.J.,Christianson, D.W.
(2017)  ACS Chem. Biol.  12 : 2281 - 2286

PubMed: 28846375
DOI: 10.1021/acschembio.7b00330

Reaction

Chain : A
UniProt : Q9BY41 (HDAC8_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl- [histone] 3.5.1.98 PubMed:10748112, PubMed:10922473, PubMed:10926844, PubMed:28497810
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H2O + N(6)-acetyl-L-lysyl-[protein] = acetate + L-lysyl- [protein] - PubMed:22885700
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H2O + N(6)-(2E)-butenoyl-L-lysyl-[protein] = (2E)-2-butenoate + L-lysyl-[protein] - PubMed:28497810
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