› 3shy

X-ray diffraction
2.65Å resolution

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

Released:
DOI: 10.2210/pdb3shy/pdb
PDB entry 3shy coloured by chain, front view.
PDB entry 3shy coloured by chain, side view.
PDB entry 3shy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Utilization of halogen bond in lead optimization: a case study of rational design of potent phosphodiesterase type 5 (PDE5) inhibitors.
Xu Z, Liu Z, Chen T, Chen T, Wang Z, Tian G, Shi J, Wang X, Lu Y, Yan X, Wang G, Jiang H, Chen K, Wang S, Xu Y, Shen J, Zhu W
J Med Chem 54 5607-11 (2011)
PMID: 21714539

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

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P3121
Unit cell:
a: 74.458Å b: 74.458Å c: 131.926Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.214 0.211 0.259
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Halogen bonding for rational drug design and new drug discovery.
Lu et al. (2012)
5 more

2 mentions without citation

A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.
Poznański et al. (2014)
1 more