4MD6 image
Entry Detail
PDB ID:
4MD6
Title:
Crystal structure of PDE5 in complex with inhibitor 5R
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2013-08-22
Release Date:
2014-07-09
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:cGMP-specific 3',5'-cyclic phosphodiesterase
Chain IDs:A
Chain Length:326
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Discovery of 3-(4-hydroxybenzyl)-1-(thiophen-2-yl)chromeno[2,3-c]pyrrol-9(2H)-one as a phosphodiesterase-5 inhibitor and its complex crystal structure.
Biochem Pharmacol 89 86 98 (2014)
PMID: 24565909 DOI: 10.1016/j.bcp.2014.02.013

Abstact

Phosphodiesterase-5 (PDE5) inhibitors have been approved for the treatment of erectile dysfunction and pulmonary hypertension, but enthusiasm on discovery of PDE5 inhibitors continues for their potential new applications. Reported here is discovery of a series of new PDE5 inhibitors by structure-based design, molecular docking, chemical synthesis, and enzymatic characterization. The best compound, 3-(4-hydroxybenzyl)-1-(thiophen-2-yl)chromeno[2,3-c]pyrrol-9(2H)-one (57), has an IC₅₀ of 17 nM against the PDE5 catalytic domain and good selectivity over other PDE families. The crystal structure of the PDE5 catalytic domain in complex with 57 was determined at 2Å resolution and showed that 57 occupies the same pocket as other PDE5 inhibitors, but has a different binding pattern in detail. On the basis of the binding pattern of 57, a novel scaffold can be proposed as a candidate of PDE inhibitors.

Legend

Protein

Chemical

Disease

Primary Citation of related structures