› 4oex

X-ray diffraction
2.14Å resolution

Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors

Released:
DOI: 10.2210/pdb4oex/pdb
PDB entry 4oex coloured by chain, front view.
PDB entry 4oex coloured by chain, side view.
PDB entry 4oex coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Thermodynamic and structural characterization of halogen bonding in protein-ligand interactions: a case study of PDE5 and its inhibitors.
Ren J, He Y, Chen W, Chen T, Wang G, Wang Z, Xu Z, Luo X, Zhu W, Jiang H, Shen J, Xu Y
J Med Chem 57 3588-93 (2014)
PMID: 24702184

Function and Biology Details

Reaction catalysed: 
Guanosine 3',5'-cyclic phosphate + H(2)O = guanosine 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-131208 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
cGMP-specific 3',5'-cyclic phosphodiesterase Chain: A
Molecule details ›
Chain: A
Length: 347 amino acids
Theoretical weight: 40.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O76074 (Residues: 535-860; Coverage: 37%)
Gene names: PDE5, PDE5A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand 5EO 1 x 5EO
Ligand ZN 1 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P3121
Unit cell:
a: 74.03Å b: 74.03Å c: 131.95Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.193 0.191 0.24
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Applications of isothermal titration calorimetry - the research and technical developments from 2011 to 2015.
Falconer RJ. (2016)
6 other articles

2 mentions without citation

Identification of a Novel 1,2,3,4-Tetrahydrobenzo[b][1,6]naphthyridine Analogue as a Potent Phosphodiesterase 5 Inhibitor with Improved Aqueous Solubility for the Treatment of Alzheimer's Disease.
Fiorito et al. (2017)
1 more