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 

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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:  
    2H40, 2H42, 2H44

  • 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 unliganded PDE5A1 and its complexes with sildenafil or icarisid II ...

    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
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(by identity cutoff)  |  3D 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
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
PHAROS:  O76074
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76074
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VIA
Query on VIA
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth 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 Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
VIA BindingDB:  2H42 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)
PDBBind:  2H42 IC50: 2.4 (nM) from 1 assay(s)
Binding MOAD:  2H42 IC50: 2.4 (nM) from 1 assay(s)
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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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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