› 8g43

X-ray diffraction
1.55Å resolution

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(methylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid

Released:
DOI: 10.2210/pdb8g43/pdb
PDB entry 8g43 coloured by chain, front view.
PDB entry 8g43 coloured by chain, side view.
PDB entry 8g43 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6.
Harding RJ, Franzoni I, Mann MK, Szewczyk MM, Mirabi B, Ferreira de Freitas R, Owens DDG, Ackloo S, Scheremetjew A, Juarez-Ornelas KA, Sanichar R, Baker RJ, Dank C, Brown PJ, Barsyte-Lovejoy D, Santhakumar V, Schapira M, Lautens M, Arrowsmith CH
OpenAccess logo J Med Chem (2023)
PMID: 37499118

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:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193657 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 6 Chain: A
Molecule details ›
Chain: A
Length: 107 amino acids
Theoretical weight: 11.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBN7 (Residues: 1109-1213; Coverage: 9%)
Gene names: HDAC6, JM21, KIAA0901
Sequence domains: Zn-finger in ubiquitin-hydrolases and other protein

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand ZU6 1 x ZU6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 40.87Å b: 44.04Å c: 55.87Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.161 0.177
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Small Molecule Screen Identifies Non-catalytic USP3 Chemical Handle.
Mann et al. (2024)

1 mention without citation

Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6.
Harding et al. (2023)