1XP0

Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Vardenafil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases.

Card, G.L.England, B.P.Suzuki, Y.Fong, D.Powell, B.Lee, B.Luu, C.Tabrizizad, M.Gillette, S.Ibrahim, P.N.Artis, D.R.Bollag, G.Milburn, M.V.Kim, S.-H.Schlessinger, J.Zhang, K.Y.J.

(2004) Structure 12: 2233-2247

  • DOI: 10.1016/j.str.2004.10.004
  • Primary Citation of Related Structures:  
    1XLZ, 1XLX, 1XM6, 1XM4, 1XMY, 1XMU, 1XN0, 1XOZ, 1XP0, 1XON

  • PubMed Abstract: 
  • Phosphodiesterases (PDEs) comprise a large family of enzymes that catalyze the hydrolysis of cAMP or cGMP and are implicated in various diseases. We describe the high-resolution crystal structures of the catalytic domains of PDE4B, PDE4D, and PDE5A w ...

    Phosphodiesterases (PDEs) comprise a large family of enzymes that catalyze the hydrolysis of cAMP or cGMP and are implicated in various diseases. We describe the high-resolution crystal structures of the catalytic domains of PDE4B, PDE4D, and PDE5A with ten different inhibitors, including the drug candidates cilomilast and roflumilast, for respiratory diseases. These cocrystal structures reveal a common scheme of inhibitor binding to the PDEs: (i) a hydrophobic clamp formed by highly conserved hydrophobic residues that sandwich the inhibitor in the active site; (ii) hydrogen bonding to an invariant glutamine that controls the orientation of inhibitor binding. A scaffold can be readily identified for any given inhibitor based on the formation of these two types of conserved interactions. These structural insights will enable the design of isoform-selective inhibitors with improved binding affinity and should facilitate the discovery of more potent and selective PDE inhibitors for the treatment of a variety of diseases.


    Organizational Affiliation

    Plexxikon, Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesteraseA364Homo sapiensMutation(s): 17 
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VDN
Query on VDN

Download CCD File 
A
2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
C23 H32 N6 O4 S
SECKRCOLJRRGGV-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 %)
VDNIC50:  0.20000000298023224   nM  BindingDB
VDNIC50:  0.17000000178813934   nM  BindingDB
VDNIC50 :  1   nM  PDBBind
VDNIC50:  0.7099999785423279   nM  BindingDB
VDNKi:  0.699999988079071   nM  BindingDB
VDNIC50:  1   nM  BindingDB
VDNIC50:  0.8899999856948853   nM  BindingDB
VDNKi:  1   nM  BindingDB
VDNIC50:  0.5   nM  BindingDB
VDNIC50:  0.699999988079071   nM  BindingDB
VDNIC50:  1   nM  BindingDB
VDNIC50:  1   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.662α = 90
b = 89.662β = 90
c = 222.002γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance