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 

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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 the treatment of various diseases, including heart failure, depression, asthma, inflammation and erectile dysfunction ...

    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 phosphodiesteraseA, B324Homo sapiensMutation(s): 0 
Gene Names: PDE5APDE5
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
PHAROS:  O76074
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIA (Subject of Investigation/LOI)
Query on CIA

Download Ideal Coordinates CCD File 
E [auth A], H [auth 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 Ideal Coordinates CCD File 
C [auth A], F [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CIA BindingDB:  1UDU Ki: min: 5, max: 10 (nM) from 3 assay(s)
IC50: min: 1.2, max: 12 (nM) from 13 assay(s)
EC50: 78 (nM) from 1 assay(s)
PDBBind:  1UDU Kd: 0.9 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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