› 6ht8

X-ray diffraction
2.5Å resolution

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 3

Released:
DOI: 10.2210/pdb6ht8/pdb
PDB entry 6ht8 coloured by chain, front view.
PDB entry 6ht8 coloured by chain, side view.
PDB entry 6ht8 coloured by chain, top view.
Source organism: Schistosoma mansoni
Primary publication:
Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants.
Marek M, Shaik TB, Heimburg T, Chakrabarti A, Lancelot J, Ramos-Morales E, Da Veiga C, Kalinin D, Melesina J, Robaa D, Schmidtkunz K, Suzuki T, Holl R, Ennifar E, Pierce RJ, Jung M, Sippl W, Romier C
J Med Chem 61 10000-10016 (2018)
PMID: 30347148

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107599 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
histone deacetylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 447 amino acids
Theoretical weight: 50.58 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

5 bound ligands:
Ligand ZN 4 x ZN
Ligand K 8 x K
Ligand GQE 4 x GQE
Ligand GOL 8 x GOL
Ligand DMF 8 x DMF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P1
Unit cell:
a: 70.788Å b: 70.921Å c: 98.342Å
α: 77.9° β: 75.58° γ: 85.33°
R-values:
R R work R free
0.162 0.158 0.236
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Next-generation of selective histone deacetylase inhibitors.
Yang et al. (2019)
6 more

1 mention without citation

Binding Free Energy (BFE) Calculations and Quantitative Structure-Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 (smHDAC8) Inhibitors.
Simoben et al. (2021)