› 3sfh

X-ray diffraction
2.7Å resolution

Crystal Structure of Human HDAC8 Inhibitor Complex, an Amino Acid Derived Inhibitor

Released:
DOI: 10.2210/pdb3sfh/pdb
PDB entry 3sfh coloured by chain, front view.
PDB entry 3sfh coloured by chain, side view.
PDB entry 3sfh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors.
Whitehead L, Dobler MR, Radetich B, Zhu Y, Atadja PW, Claiborne T, Grob JE, McRiner A, Pancost MR, Patnaik A, Shao W, Shultz M, Tichkule R, Tommasi RA, Vash B, Wang P, Stams T
Bioorg Med Chem 19 4626-34 (2011)
PMID: 21723733

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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189815 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 8 Chain: A
Molecule details ›
Chain: A
Length: 378 amino acids
Theoretical weight: 41.89 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9BY41 (Residues: 1-377; Coverage: 100%)
Gene names: CDA07, HDAC8, HDACL1
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

4 bound ligands:
Ligand K 2 x K
Ligand ZN 1 x ZN
Ligand ACT 3 x ACT
Ligand 1DI 1 x 1DI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 57.643Å b: 53.366Å c: 60.893Å
α: 90° β: 109.47° γ: 90°
R-values:
R R work R free
0.179 0.175 0.244
Expression system: Spodoptera frugiperda

Quick links

Citations

18 review citations

Targeted cancer therapy: giving histone deacetylase inhibitors all they need to succeed.
Gryder et al. (2012)
17 more

11 mentions without citation

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
10 more