2H42

Crystal structure of PDE5 in complex with sildenafil

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

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

  • 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 unligand ...

    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, University of North Carolina, Chapel Hill, 27599-7260, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesteraseA, B, C326Homo sapiensMutation(s): 0 
Gene Names: PDE5A, PDE5
EC: 3.1.4.35
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
NIH Common Fund Data Resources
PHAROS  O76074
GTEx  ENSG00000138735
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VIA
Query on VIA
Download CCD File 
A, B, C
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, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VIAIC50:  10   nM  BindingDB
VIAIC50:  53   nM  BindingDB
VIAIC50:  3.5   nM  BindingDB
VIAIC50:  188   nM  BindingDB
VIAIC50:  2.4000000953674316   nM  Binding MOAD
VIAIC50:  3   nM  BindingDB
VIAKi:  1.899999976158142   nM  BindingDB
VIAIC50:  5.900000095367432   nM  BindingDB
VIAIC50:  1.7799999713897705   nM  BindingDB
VIAIC50:  3.5999999046325684   nM  BindingDB
VIAIC50:  1.600000023841858   nM  BindingDB
VIAIC50:  75   nM  BindingDB
VIAIC50:  3.9000000953674316   nM  BindingDB
VIAIC50 :  2.4000000953674316   nM  PDBBind
VIAIC50:  4   nM  BindingDB
VIAIC50:  2.200000047683716   nM  BindingDB
VIAIC50:  11   nM  BindingDB
VIAIC50:  0.30000001192092896   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
VIAKi:  1.7999999523162842   nM  BindingDB
VIAIC50:  2.4000000953674316   nM  BindingDB
VIAIC50:  20   nM  BindingDB
VIAEC50:  8.699999809265137   nM  BindingDB
VIAEC50:  42   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
AMoREphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2006-05-23 
  • Released Date: 2006-06-06 
    • Deposition Author(s): Wang, H., Ke, H.

Revision History 

  • 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