› 6r0k

X-ray diffraction
1.15Å resolution

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS208

Released:
DOI: 10.2210/pdb6r0k/pdb
PDB entry 6r0k coloured by chain, front view.
PDB entry 6r0k coloured by chain, side view.
PDB entry 6r0k coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Discovery of a New Isoxazole-3-hydroxamate-Based Histone Deacetylase 6 Inhibitor SS-208 with Antitumor Activity in Syngeneic Melanoma Mouse Models.
Shen S, Hadley M, Ustinova K, Pavlicek J, Knox T, Noonepalle S, Tavares MT, Zimprich CA, Zhang G, Robers MB, Bařinka C, Kozikowski AP, Villagra A
J Med Chem 62 8557-8577 (2019)
PMID: 31414801

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123745 (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

4 bound ligands:
Ligand ZN 1 x ZN
Ligand K 2 x K
Ligand JNN 1 x JNN
Ligand SCN 8 x SCN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P21212
Unit cell:
a: 84.028Å b: 93.886Å c: 51.679Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.17 0.178
Expression system: Homo sapiens

Quick links

Citations

6 review citations

A patent review of histone deacetylase 6 inhibitors in neurodegenerative diseases (2014-2019).
Shen et al. (2020)
5 more

2 mentions without citation

Structural determinants of affinity and selectivity in the binding of inhibitors to histone deacetylase 6.
Osko et al. (2020)
1 more