› 7p2t

X-ray diffraction
2.3Å resolution

Tetartohedrally twinned crystal structure of Schistosoma mansoni HDAC8 in complex with a tricyclic thieno[3,2-b]indole capped hydroxamate-based inhibitor, bromine derivative

Released:
DOI: 10.2210/pdb7p2t/pdb
PDB entry 7p2t coloured by chain, front view.
PDB entry 7p2t coloured by chain, side view.
PDB entry 7p2t coloured by chain, top view.
Source organism: Schistosoma mansoni
Primary publication:
Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors.
Saccoccia F, Pozzetti L, Gimmelli R, Butini S, Guidi A, Papoff G, Giannaccari M, Brogi S, Scognamiglio V, Gemma S, Ruberti G, Campiani G
OpenAccess logo J Biol Chem 102375 (2022)
PMID: 35970392

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:
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: 440 amino acids
Theoretical weight: 49.83 KDa
Source organism: Schistosoma mansoni
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A5H660 (Residues: 1-440; Coverage: 100%)
Gene name: HDAC8
Sequence domains: Histone deacetylase domain

Ligands and Environments

5 bound ligands:
Ligand ZN 4 x ZN
Ligand K 10 x K
Ligand 4VX 4 x 4VX
Ligand 144 2 x 144
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 11.2C
Spacegroup: C2
Unit cell:
a: 99.205Å b: 99.003Å c: 178.585Å
α: 90° β: 91.3° γ: 90°
R-values:
R R work R free
0.279 not available 0.294
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Computational Insights into Natural Antischistosomal Metabolites as SmHDAC8 Inhibitors: Molecular Docking, ADMET Profiling, and Molecular Dynamics Simulation.
Alzain et al. (2023)

1 mention without citation

Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors.
Saccoccia et al. (2022)