› 4i9z

X-ray diffraction
2.08Å resolution

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

Released:
DOI: 10.2210/pdb4i9z/pdb
PDB entry 4i9z coloured by chain, front view.
PDB entry 4i9z coloured by chain, side view.
PDB entry 4i9z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Exploration of the 5-bromopyrimidin-4(3H)-ones as potent inhibitors of PDE5.
Gong X, Wang G, Ren J, Liu Z, Wang Z, Chen T, Yang X, Jiang X, Shen J, Jiang H, Aisa HA, Xu Y, Li J
Bioorg Med Chem Lett 23 4944-7 (2013)
PMID: 23867165

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
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

4 bound ligands:
Ligand 5BA 1 x 5BA
Ligand ZN 1 x ZN
Ligand MG 1 x MG
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P3121
Unit cell:
a: 74.85Å b: 74.85Å c: 132.28Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.202 0.201 0.237
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Application of ITC-Based Characterization of Thermodynamic and Kinetic Association of Ligands With Proteins in Drug Design.
Su et al. (2018)
2 more

2 mentions without citation

Advancements in Phosphodiesterase 5 Inhibitors: Unveiling Present and Future Perspectives.
ElHady et al. (2023)
1 more