› 5b8d

X-ray diffraction
1.05Å resolution

Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Released:
DOI: 10.2210/pdb5b8d/pdb
PDB entry 5b8d coloured by chain, front view.
PDB entry 5b8d coloured by chain, side view.
PDB entry 5b8d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin.
Harding RJ, Ferreira de Freitas R, Collins P, Franzoni I, Ravichandran M, Ouyang H, Juarez-Ornelas KA, Lautens M, Schapira M, von Delft F, Santhakumar V, Arrowsmith CH
J Med Chem 60 9090-9096 (2017)
PMID: 29019676

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
Sequence domains:

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 BL21(DE3)
UniProt:
  • Canonical: Q9UBN7 (Residues: 1109-1213; Coverage: 9%)
Gene names: HDAC6, JM21, KIAA0901
Sequence domains: Zn-finger in ubiquitin-hydrolases and other protein
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

5 bound ligands:
Ligand ZN 3 x ZN
Ligand FMT 2 x FMT
Ligand 6T4 1 x 6T4
Ligand UNX 36 x UNX
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 41.434Å b: 44.157Å c: 56.549Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.129 0.128 0.146
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Regulation of Thermogenic Adipocyte Differentiation and Adaptive Thermogenesis Through Histone Acetylation.
Ong et al. (2020)
6 other articles

1 mention without citation

Emodin inhibits HDAC6 mediated NLRP3 signaling and relieves chronic inflammatory pain in mice.
Cheng et al. (2024)