We've built a new version of this page with an interactive 3D viewer. Try it out in beta and help us improve:

› 6fu1

X-ray diffraction
1.55Å resolution

Crystal structure of Schistosoma mansoni HDAC8 complexed with a n-alkyl hydroxamate

Released:
DOI: 10.2210/pdb6fu1/pdb
Model geometry
Fit model/data
PDB entry 6fu1 coloured by chain, front view.
PDB entry 6fu1 coloured by chain, side view.
PDB entry 6fu1 coloured by chain, top view.
Source organism: Schistosoma mansoni
Primary publication:
A Novel Class of Schistosoma mansoni Histone Deacetylase 8 (HDAC8) Inhibitors Identified by Structure-Based Virtual Screening and In Vitro Testing.
Simoben CV, Robaa D, Chakrabarti A, Schmidtkunz K, Marek M, Lancelot J, Kannan S, Melesina J, Shaik TB, Pierce RJ, Romier C, Jung M, Sippl W
OpenAccess logo Molecules 23 (2018)
PMID: 29498707

Function and Biology Details

Reaction catalysed: 
N(6)-acetyl-L-lysyl-[histone] + H2O = L-lysyl-[histone] + acetate.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107598 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
histone deacetylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 446 amino acids
Theoretical weight: 50.44 KDa
Source organism: Schistosoma mansoni
Expression system: Escherichia coli
UniProt:
  • Canonical: A5H660 (Residues: 1-440; Coverage: 100%)
Gene name: HDAC8
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand K 8 x K
Ligand E7Q 4 x E7Q
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P1
Unit cell:
a: 70.71Å b: 70.69Å c: 99.19Å
α: 75.33° β: 77.78° γ: 84.8°
R-values:
R R work R free
0.201 0.199 0.223
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention.
Ruzic et al. (2022)
3 more

1 mention without citation

A Novel Class of Schistosoma mansoni Histone Deacetylase 8 (HDAC8) Inhibitors Identified by Structure-Based Virtual Screening and In Vitro Testing.
Simoben et al. (2018)