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
  • Primary Citation of Related Structures:  
    3B2R

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesteraseAB330Homo sapiensMutation(s): 0 
Gene Names: PDE5APDE5
EC: 3.1.4.35
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
NIH Common Fund Data Resources
PHAROS  O76074
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VDN
Query on VDN

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
C23 H32 N6 O4 S
SECKRCOLJRRGGV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VDNIC50:  0.7099999785423279   nM  BindingDB
VDNIC50:  0.17000000178813934   nM  BindingDB
VDNKi:  0.699999988079071   nM  BindingDB
VDNIC50:  0.20000000298023224   nM  BindingDB
VDNIC50:  0.5   nM  BindingDB
VDNIC50:  0.8899999856948853   nM  BindingDB
VDNIC50:  1   nM  BindingDB
VDNIC50:  0.699999988079071   nM  BindingDB
VDNKi:  1   nM  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
b = 87.822β = 90
c = 138.472γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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