› 8bjk

X-ray diffraction
1.35Å resolution

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor CPD11352

Released:
DOI: 10.2210/pdb8bjk/pdb
PDB entry 8bjk coloured by chain, front view.
PDB entry 8bjk coloured by chain, side view.
PDB entry 8bjk coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6).
Motlová L, Šnajdr I, Kutil Z, Andris E, Ptáček J, Novotná A, Nováková Z, Havlínová B, Tueckmantel W, Dráberová H, Majer P, Schutkowski M, Kozikowski A, Rulíšek L, Bařinka C
OpenAccess logo ACS Chem Biol 18 1594-1610 (2023)
PMID: 37392419

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-514703 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UBP-type domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 359 amino acids
Theoretical weight: 39.9 KDa
Source organism: Danio rerio
Expression system: Homo sapiens
UniProt:
  • Canonical: F8W4B7 (Residues: 440-798; Coverage: 33%)
Gene name: hdac6
Sequence domains: Histone deacetylase domain

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand K 2 x K
Ligand QXF 1 x QXF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER METALJET
Unit cell:
a: 51.49Å b: 83.78Å c: 94.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.207
Expression system: Homo sapiens

Quick links

Citations

2 citation in other articles

Difluoromethyl-1,3,4-oxadiazoles Are Selective, Mechanism-Based, and Essentially Irreversible Inhibitors of Histone Deacetylase 6.
König et al. (2023)
1 more