3B2R

Crystal Structure of PDE5A1 catalytic domain in complex with Vardenafil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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, S.H.Ke, H.

(2008) Mol.Pharmacol. 73: 104-110

  • DOI: 10.1124/mol.107.040212

  • PubMed Abstract: 
  • Vardenafil has higher affinity to phosphodiesterase-5 (PDE5) than sildenafil and lower administered dosage for the treatment of erectile dysfunction. However, the molecular basis for these differences is puzzling because two drugs have similar chemic ...

    Vardenafil has higher affinity to phosphodiesterase-5 (PDE5) than sildenafil and lower administered dosage for the treatment of erectile dysfunction. However, the molecular basis for these differences is puzzling because two drugs have similar chemical structures. Reported here is a crystal structure of the fully active and nonmutated PDE5A1 catalytic domain in complex with vardenafil. The structure shows that the conformation of the H-loop in the PDE5A1-vardenafil complex is different from those of any known structures of the unliganded PDE5 and its complexes with the inhibitors. In addition, the molecular configuration of vardenafil differs from that of sildenafil when bound to PDE5. It is noteworthy that the binding of vardenafil causes loss of the divalent metal ions that have been observed in all the previously published PDE structures. The conformational variation of both PDE5 and the inhibitors provides structural insight into the different potencies of the drugs.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, 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, B
330Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VDN
Query on VDN

Download SDF File 
Download CCD File 
A, B
2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
VARDENAFIL, LEVITRA
C23 H32 N6 O4 S
SECKRCOLJRRGGV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VDNIC50: 0.2 - 1 nM (100) BINDINGDB
VDNKi: 1 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.922α = 90.00
b = 87.822β = 90.00
c = 138.472γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
AMoREphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance