› 4htx

X-ray diffraction
1.9Å resolution

Crystal structure of PDE2 catalytic domain in complex with BAY60-7550

Released:
DOI: 10.2210/pdb4htx/pdb
PDB entry 4htx coloured by chain, front view.
PDB entry 4htx coloured by chain, side view.
PDB entry 4htx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
X-ray crystal structure of phosphodiesterase 2 in complex with a highly selective, nanomolar inhibitor reveals a binding-induced pocket important for selectivity.
Zhu J, Yang Q, Dai D, Huang Q
J Am Chem Soc 135 11708-11 (2013)
PMID: 23899287

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126261 (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: 39.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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

3 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 4 x MG
Ligand 19F 4 x 19F
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P1
Unit cell:
a: 56.26Å b: 73.82Å c: 92.47Å
α: 109.59° β: 91.93° γ: 90.88°
R-values:
R R work R free
0.175 0.173 0.227
Expression system: Escherichia coli

Quick links

Citations

5 review citations

In Search of Enzymes with a Role in 3', 5'-Cyclic Guanosine Monophosphate Metabolism in Plants.
Gross et al. (2016)
4 more

8 mentions without citation

Identification of a PDE4-Specific Pocket for the Design of Selective Inhibitors.
Feng et al. (2018)
7 more