› 8hub

X-ray diffraction
3.25Å resolution

AMP deaminase 2 in complex with an inhibitor

Released:
DOI: 10.2210/pdb8hub/pdb
Model geometry
Fit model/data
PDB entry 8hub coloured by chain, front view.
PDB entry 8hub coloured by chain, side view.
PDB entry 8hub coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The discovery of 3,3-dimethyl-1,2,3,4-tetrahydroquinoxaline-1-carboxamides as AMPD2 inhibitors with a novel mechanism of action.
Kitao Y, Saito T, Watanabe S, Ohe Y, Takahashi K, Akaki T, Adachi T, Doi S, Yamanaka K, Murai Y, Oba M, Suzuki T
Bioorg Med Chem Lett 80 129110 (2023)
PMID: 36563792

Function and Biology Details

Reaction catalysed: 
AMP + H(2)O = IMP + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169556 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
AMP deaminase 2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 678 amino acids
Theoretical weight: 78.75 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q01433 (Residues: 157-825; Coverage: 81%)
Gene name: AMPD2
Sequence domains: AMP deaminase

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand N4X 3 x N4X
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2221
Unit cell:
a: 124.516Å b: 162.533Å c: 289.758Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.259 0.258 0.276
Expression system: Spodoptera frugiperda

Quick links

Citations

1 citations in other articles

Frameshift Variant in AMPD2 in Cirneco dell'Etna Dogs with Retinopathy and Tremors.
Murgiano et al. (2024)

1 mention without citation

Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review.
Ghasemi et al. (2024)