› 7zzr

X-ray diffraction
2.17Å resolution

HDAC2 in complex with inhibitory ligand

Released:
DOI: 10.2210/pdb7zzr/pdb
Model geometry
Fit model/data
PDB entry 7zzr coloured by chain, front view.
PDB entry 7zzr coloured by chain, side view.
PDB entry 7zzr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Fragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor.
Tamanini E, Miyamura S, Buck IM, Cons BD, Dawson L, East C, Futamura T, Goto S, Griffiths-Jones C, Hashimoto T, Heightman TD, Ishikawa S, Ito H, Kaneko Y, Kawato T, Kondo K, Kurihara N, McCarthy JM, Mori Y, Nagase T, Nakaishi Y, Reeks J, Sato A, Schöpf P, Tai K, Tamai T, Tisi D, Woolford AJ
ACS Med Chem Lett 13 1591-1597 (2022)
PMID: 36262388

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-187745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 498 amino acids
Theoretical weight: 56.56 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92769 (Residues: 1-488; Coverage: 100%)
Gene name: HDAC2
Sequence domains: Histone deacetylase domain

Ligands and Environments

8 bound ligands:
Ligand ZN 3 x ZN
Ligand CA 3 x CA
Ligand NA 3 x NA
Ligand EDO 10 x EDO
Ligand KJN 3 x KJN
Ligand NHE 1 x NHE
Ligand PG4 1 x PG4
Ligand PEG 5 x PEG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 91.991Å b: 97.7Å c: 138.849Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.188 0.247
Expression system: Spodoptera frugiperda

Quick links

Citations

1 review citation

Medicinal chemistry advances in targeting class I histone deacetylases.
Abdallah et al. (2023)

2 mentions without citation

Developing Nanostructured Ti Alloys for Innovative Implantable Medical Devices.
Valiev et al. (2020)
1 more