Crystal structure of Human Phosphodiesterase 5 complexed with Sildenafil(Viagra)

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules

Sung, B.-J.Hwang, K.Y.Jeon, Y.H.Lee, J.I.Heo, Y.-S.Kim, J.H.Moon, J.Yoon, J.M.Hyun, Y.-L.Kim, E.Eum, S.J.Park, S.-Y.Lee, J.-O.Lee, T.G.Ro, S.Cho, J.M.

(2003) Nature 425: 98-102

  • DOI: https://doi.org/10.1038/nature01914
  • Primary Citation of Related Structures:  
    1UDT, 1UDU, 1UHO

  • PubMed Abstract: 

    Phosphodiesterases (PDEs) are a superfamily of enzymes that degrade the intracellular second messengers cyclic AMP and cyclic GMP. As essential regulators of cyclic nucleotide signalling with diverse physiological functions, PDEs are drug targets for the treatment of various diseases, including heart failure, depression, asthma, inflammation and erectile dysfunction. Of the 12 PDE gene families, cGMP-specific PDE5 carries out the principal cGMP-hydrolysing activity in human corpus cavernosum tissue. It is well known as the target of sildenafil citrate (Viagra) and other similar drugs for the treatment of erectile dysfunction. Despite the pressing need to develop selective PDE inhibitors as therapeutic drugs, only the cAMP-specific PDE4 structures are currently available. Here we present the three-dimensional structures of the catalytic domain (residues 537-860) of human PDE5 complexed with the three drug molecules sildenafil, tadalafil (Cialis) and vardenafil (Levitra). These structures will provide opportunities to design potent and selective PDE inhibitors with improved pharmacological profiles.

  • Organizational Affiliation

    Division of Drug Discovery, CrystalGenomics, Inc., Daedeok Biocommunity, Jeonmin-dong, Yuseong-gu, Daejeon, 305-390, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase324Homo sapiensMutation(s): 0 
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 
C22 H30 N6 O4 S
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Query on MG

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
VIA BindingDB:  1UDT 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)
Binding MOAD:  1UDT Kd: 0.5 (nM) from 1 assay(s)
PDBBind:  1UDT Kd: 0.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.122α = 90
b = 155.632β = 90
c = 89.896γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Structure summary