1UDU

Crystal structure of Human Phosphodiesterase 5 complexed with tadalafil(Cialis)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.374 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

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
  • Primary Citation of Related Structures:  
    1UDU, 1UDT, 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesteraseAB324Homo 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)
Explore O76074 
Go to UniProtKB:  O76074
NIH Common Fund Data Resources
PHAROS  O76074
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIA
Query on CIA

Download CCD File 
A, B
6-BENZO[1,3]DIOXOL-5-YL-2-METHYL-2,3,6,7,12,12A-HEXAHYDRO-PYRAZINO[1',2':1,6]PYRIDO[3,4-B]INDOLE-1,4-DIONE
C22 H19 N3 O4
WOXKDUGGOYFFRN-IIBYNOLFSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CIAIC50:  5   nM  BindingDB
CIAIC50:  3.200000047683716   nM  BindingDB
CIAEC50:  78   nM  BindingDB
CIAIC50:  9.399999618530273   nM  BindingDB
CIAIC50:  4   nM  BindingDB
CIAKi:  5   nM  BindingDB
CIAIC50:  12   nM  BindingDB
CIAKi:  5.199999809265137   nM  BindingDB
CIAIC50:  4.699999809265137   nM  BindingDB
CIAKi:  10   nM  BindingDB
CIAIC50:  1.2999999523162842   nM  BindingDB
CIAIC50:  3.299999952316284   nM  BindingDB
CIAIC50:  6.699999809265137   nM  BindingDB
CIAIC50:  3   nM  BindingDB
CIAKd :  0.8999999761581421   nM  PDBBind
CIAIC50:  1.2000000476837158   nM  BindingDB
CIAIC50:  5   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.374 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.352α = 90
b = 48.561β = 117.28
c = 123.863γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata 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