› 6c7e

X-ray diffraction
1.43Å resolution

Crystal structure of human phosphodiesterase 2A with 1-(2-chlorophenyl)-N,4-dimethyl-[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide

Released:
DOI: 10.2210/pdb6c7e/pdb
PDB entry 6c7e coloured by chain, front view.
PDB entry 6c7e coloured by chain, side view.
PDB entry 6c7e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mathematical and Structural Characterization of Strong Nonadditive Structure-Activity Relationship Caused by Protein Conformational Changes.
Gomez L, Xu R, Sinko W, Selfridge B, Vernier W, Ly K, Truong R, Metz M, Marrone T, Sebring K, Yan Y, Appleton B, Aertgeerts K, Massari ME, Breitenbucher JG
J Med Chem 61 7754-7766 (2018)
PMID: 30070482

Function and Biology Details

Reaction catalysed: 
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126260 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
cGMP-dependent 3',5'-cyclic phosphodiesterase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 342 amino acids
Theoretical weight: 39.91 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O00408 (Residues: 579-917; Coverage: 36%)
Gene name: PDE2A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand EOG 4 x EOG
Ligand ZN 4 x ZN
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P1
Unit cell:
a: 55.96Å b: 72.65Å c: 90.73Å
α: 109.11° β: 91.28° γ: 91.2°
R-values:
R R work R free
0.176 0.174 0.201
Expression system: Spodoptera frugiperda

Quick links

Citations

7 citation in other articles

Nonadditivity in public and inhouse data: implications for drug design.
Gogishvili et al. (2021)
6 more

1 mention without citation

Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].
Hahn et al. (2022)