4MD6

Crystal structure of PDE5 in complex with inhibitor 5R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1016/j.bcp.2014.02.013

  • 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 o ...

    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.


    Organizational Affiliation

    School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599-7260, USA.,School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China. Electronic address: luohb77@mail.sysu.edu.cn.,School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China. Electronic address: phsbxzh@mail.sysu.edu.cn.,School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China; Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599-7260, USA. Electronic address: hke@med.unc.edu.,School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.,Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599-7260, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-specific 3',5'-cyclic phosphodiesterase
A
326Homo sapiensMutation(s): 0 
Gene Names: PDE5A (PDE5)
EC: 3.1.4.35
Find proteins for O76074 (Homo sapiens)
Go to Gene View: PDE5A
Go to UniProtKB:  O76074
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
24E
Query on 24E

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Download CCD File 
A
3-(4-hydroxybenzyl)-1-(thiophen-2-yl)chromeno[2,3-c]pyrrol-9(2H)-one
C22 H15 N O3 S
GPIHPADNHDARBD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
24EIC50: 17 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.106α = 90.00
b = 74.106β = 90.00
c = 132.344γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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