› 6tcy

X-ray diffraction
1.6Å resolution

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS555

Released:
DOI: 10.2210/pdb6tcy/pdb
PDB entry 6tcy coloured by chain, front view.
PDB entry 6tcy coloured by chain, side view.
PDB entry 6tcy coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Rational Design of Suprastat: A Novel Selective Histone Deacetylase 6 Inhibitor with the Ability to Potentiate Immunotherapy in Melanoma Models.
Noonepalle S, Shen S, Ptáček J, Tavares MT, Zhang G, Stránský J, Pavlíček J, Ferreira GM, Hadley M, Pelaez G, Bařinka C, Kozikowski AP, Villagra A
J Med Chem 63 10246-10262 (2020)
PMID: 32815366

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 Chains: AAA, BBB
Molecule details ›
Chains: AAA, BBB
Length: 359 amino acids
Theoretical weight: 39.9 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: F8W4B7 (Residues: 440-798; Coverage: 33%)
Gene name: hdac6
Sequence domains: Histone deacetylase domain

Ligands and Environments

9 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
Ligand N28 2 x N28
Ligand EDO 7 x EDO
Ligand TOE 1 x TOE
Ligand GOL 1 x GOL
Ligand CL 1 x CL
Ligand MXE 1 x MXE
Ligand DMS 1 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P21
Unit cell:
a: 54.809Å b: 83.811Å c: 86.092Å
α: 90° β: 97.971° γ: 90°
R-values:
R R work R free
0.192 0.191 0.23
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Combining histone deacetylase inhibitors (HDACis) with other therapies for cancer therapy.
Zhou et al. (2021)
3 more