› 6wbw

X-ray diffraction
1.46Å resolution

Structure of Human HDAC2 in complex with an ethyl ketone inhibitor

Released:
DOI: 10.2210/pdb6wbw/pdb
PDB entry 6wbw coloured by chain, front view.
PDB entry 6wbw coloured by chain, side view.
PDB entry 6wbw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of ethyl ketone-based HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation.
Yu W, Liu J, Yu Y, Zhang V, Clausen D, Kelly J, Wolkenberg S, Beshore D, Duffy JL, Chung CC, Myers RW, Klein DJ, Fells J, Holloway K, Wu J, Wu G, Howell BJ, Barnard RJO, Kozlowski J
Bioorg Med Chem Lett 30 127197 (2020)
PMID: 32331932

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-187745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 376 amino acids
Theoretical weight: 43.06 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92769 (Residues: 1-376; Coverage: 77%)
Gene name: HDAC2
Sequence domains: Histone deacetylase domain

Ligands and Environments

4 bound ligands:
Ligand TV1 3 x TV1
Ligand ZN 3 x ZN
Ligand CA 6 x CA
Ligand PEG 6 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 91.97Å b: 98.28Å c: 139.05Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.172 0.197
Expression system: Spodoptera frugiperda

Quick links

Citations

2 review citations

Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention.
Ruzic et al. (2022)
1 more

6 mentions without citation

Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases.
Frühauf et al. (2021)
5 more