› 6b97

X-ray diffraction
1.76Å resolution

Crystal structure of PDE2 in complex with complex 9

Released:
DOI: 10.2210/pdb6b97/pdb
PDB entry 6b97 coloured by chain, front view.
PDB entry 6b97 coloured by chain, side view.
PDB entry 6b97 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The identification of a novel lead class for phosphodiesterase 2 inhibition by fragment-based drug design.
Forster AB, Abeywickrema P, Bunda J, Cox CD, Cabalu TD, Egbertson M, Fay J, Getty K, Hall D, Kornienko M, Lu J, Parthasarathy G, Reid J, Sharma S, Shipe WD, Smith SM, Soisson S, Stachel SJ, Su HP, Wang D, Berger R
Bioorg Med Chem Lett 27 5167-5171 (2017)
PMID: 29113762

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
Molecule details ›
Chains: A, B
Length: 373 amino acids
Theoretical weight: 43.69 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O00408 (Residues: 578-919; Coverage: 36%)
Gene name: PDE2A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 2 x MG
Ligand CZY 2 x CZY
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 72.27Å b: 96.07Å c: 102.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.22
Expression system: Spodoptera frugiperda

Quick links

Citations

1 review citation

Put a ring on it: application of small aliphatic rings in medicinal chemistry.
Bauer et al. (2021)
2 other articles

2 mentions without citation

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