› 3b2r

X-ray diffraction
2.07Å resolution

Crystal Structure of PDE5A1 catalytic domain in complex with Vardenafil

Released:
DOI: 10.2210/pdb3b2r/pdb
PDB entry 3b2r coloured by chain, front view.
PDB entry 3b2r coloured by chain, side view.
PDB entry 3b2r coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Conformational variations of both phosphodiesterase-5 and inhibitors provide the structural basis for the physiological effects of vardenafil and sildenafil.
Wang H, Ye M, Robinson H, Francis SH, Ke H
Mol Pharmacol 73 104-10 (2008)
PMID: 17959709

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 domain:

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 330 amino acids
Theoretical weight: 38.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
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

1 bound ligand:
Ligand VDN 2 x VDN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 68.922Å b: 87.822Å c: 138.472Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 0.248
Expression system: Escherichia coli BL21

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Citations

3 review citations

Advances in targeting cyclic nucleotide phosphodiesterases.
Maurice et al. (2014)
2 more

4 mentions without citation

Conformational variations of both phosphodiesterase-5 and inhibitors provide the structural basis for the physiological effects of vardenafil and sildenafil.
Wang et al. (2008)
3 more