Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.35 kDa 
• Atom Count: 2523 
• Modelled Residue Count: 299 
• Deposited Residue Count: 326 
• Unique protein chains: 1

4MD6

Crystal structure of PDE5 in complex with inhibitor 5R

• PDB DOI: 10.2210/pdb4MD6/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-22 Released: 2014-07-09 
• Deposition Author(s): Cui, W., Huang, M., Shao, Y., Luo, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

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.

Shang, N.N., Shao, Y.X., Cai, Y.H., Guan, M., Huang, M., Cui, W., He, L., Yu, Y.J., Huang, L., Li, Z., Bu, X.Z., Ke, H., Luo, H.B.

(2014) Biochem Pharmacol 89: 86-98

• PubMed: 24565909 
• DOI: 10.1016/j.bcp.2014.02.013
• Primary Citation of Related Structures:  
  4MD6


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase	A	326	Homo sapiens	Mutation(s): 0  Gene Names: PDE5A, PDE5 EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens) Explore O76074  Go to UniProtKB:  O76074
PHAROS:  O76074 GTEx:  ENSG00000138735

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
24E	C [auth A]	3-(4-hydroxybenzyl)-1-(thiophen-2-yl)chromeno[2,3-c]pyrrol-9(2H)-one C22 H15 N O3 S GPIHPADNHDARBD-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
24E	Binding MOAD:  4MD6	IC50: 17 (nM) from 1 assay(s)
	BindingDB:  4MD6	IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.106	α = 90
b = 74.106	β = 90
c = 132.344	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-22 
• Released Date: 2014-07-09 
Deposition Author(s): Cui, W., Huang, M., Shao, Y., Luo, H.

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release