› 6ce6

X-ray diffraction
1.6Å resolution

Structure of HDAC6 zinc-finger ubiquitin binding domain soaked with 3,3'-(benzo[1,2-d:5,4-d']bis(thiazole)-2,6-diyl)dipropionic acid

Released:
DOI: 10.2210/pdb6ce6/pdb
PDB entry 6ce6 coloured by chain, front view.
PDB entry 6ce6 coloured by chain, side view.
PDB entry 6ce6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification and Structure-Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors.
Ferreira de Freitas R, Harding RJ, Franzoni I, Ravichandran M, Mann MK, Ouyang H, Lautens M, Santhakumar V, Arrowsmith CH, Schapira M
J Med Chem 61 4517-4527 (2018)
PMID: 29741882

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

3 bound ligands:
Ligand ZN 3 x ZN
Ligand UNX 3 x UNX
Ligand EYP 1 x EYP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 40.6Å b: 45.32Å c: 55.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.172 0.196
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Pharmacological Modulation of Ubiquitin-Proteasome Pathways in Oncogenic Signaling.
Sharma et al. (2021)
2 more