Crystal structure of PDE5 in complex with sildenafil

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 

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This is version 1.3 of the entry. See complete history


Multiple Conformations of Phosphodiesterase-5: Implications for enzyme function and drug development

Wang, H.Liu, Y.Huai, Q.Cai, J.Zoraghi, R.Francis, S.H.Corbin, J.D.Robinson, H.Xin, Z.Lin, G.Ke, H.

(2006) J Biol Chem 281: 21469-21479

  • DOI: https://doi.org/10.1074/jbc.M512527200
  • Primary Citation of Related Structures:  
    2H40, 2H42, 2H44

  • PubMed Abstract: 

    Phosphodiesterase-5 (PDE5) is the target for sildenafil, vardenafil, and tadalafil, which are drugs for treatment of erectile dysfunction and pulmonary hypertension. We report here the crystal structures of a fully active catalytic domain of unliganded PDE5A1 and its complexes with sildenafil or icarisid II. These structures together with the PDE5A1-isobutyl-1-methylxanthine complex show that the H-loop (residues 660-683) at the active site of PDE5A1 has four different conformations and migrates 7-35A upon inhibitor binding. In addition, the conformation of sildenafil reported herein differs significantly from those in the previous structures of chimerically hybridized or almost inactive PDE5. Mutagenesis and kinetic analyses confirm that the H-loop is particularly important for substrate recognition and that invariant Gly(659), which immediately precedes the H-loop, is critical for optimal substrate affinity and catalytic activity.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7260.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase
A, B, C
326Homo sapiensMutation(s): 0 
Gene Names: PDE5APDE5
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
PHAROS:  O76074
GTEx:  ENSG00000138735 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76074
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on VIA

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]
C22 H30 N6 O4 S
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]
Binding Affinity Annotations 
IDSourceBinding Affinity
VIA BindingDB:  2H42 Ki: min: 1.6, max: 10 (nM) from 4 assay(s)
IC50: min: 0.3, max: 1000 (nM) from 31 assay(s)
EC50: min: 8.7, max: 1000 (nM) from 3 assay(s)
PDBBind:  2H42 IC50: 2.4 (nM) from 1 assay(s)
Binding MOAD:  2H42 IC50: 2.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.575α = 90
b = 164.575β = 90
c = 193.127γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary