1UDT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1038/nature01914
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-specific 3',5'-cyclic phosphodiesterase
A
324Homo sapiensMutation(s): 0 
Gene Names: PDE5APDE5
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (UniProt)
Find proteins for O76074 (Homo sapiens)
Go to UniProtKB:  O76074
NIH Common Fund Data Resources
PHAROS  O76074
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VIA
Query on VIA

Download CCD File 
A
5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
C22 H30 N6 O4 S
BNRNXUUZRGQAQC-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VIAIC50:  2.200000047683716   nM  BindingDB
VIAIC50:  11   nM  BindingDB
VIAIC50:  1   nM  BindingDB
VIAIC50:  1.7999999523162842   nM  BindingDB
VIAIC50:  5.599999904632568   nM  BindingDB
VIAKi:  10   nM  BindingDB
VIAIC50:  3.9000000953674316   nM  BindingDB
VIAIC50:  6.599999904632568   nM  BindingDB
VIAIC50:  8.5   nM  BindingDB
VIAIC50:  6   nM  BindingDB
VIAIC50:  2.4000000953674316   nM  BindingDB
VIAIC50:  20   nM  BindingDB
VIAIC50:  0.30000001192092896   nM  BindingDB
VIAEC50:  8.699999809265137   nM  BindingDB
VIAKi:  1.7999999523162842   nM  BindingDB
VIAEC50:  42   nM  BindingDB
VIAIC50:  10   nM  BindingDB
VIAIC50:  53   nM  BindingDB
VIAIC50:  3.5   nM  BindingDB
VIAIC50:  188   nM  BindingDB
VIAIC50:  3   nM  BindingDB
VIAKi:  1.899999976158142   nM  BindingDB
VIAIC50:  1.7799999713897705   nM  BindingDB
VIAIC50:  5.900000095367432   nM  BindingDB
VIAKd:  0.5   nM  Binding MOAD
VIAIC50:  3.5999999046325684   nM  BindingDB
VIAIC50:  1.600000023841858   nM  BindingDB
VIAIC50:  75   nM  BindingDB
VIAIC50:  3.9000000953674316   nM  BindingDB
VIAKd :  0.5   nM  PDBBind
VIAIC50:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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