1TBF

Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases

Zhang, K.Y.J.Card, G.L.Suzuki, Y.Artis, D.R.Fong, D.Gillette, S.Hsieh, D.Neiman, J.West, B.L.Zhang, C.Milburn, M.V.Kim, S.-H.Schlessinger, J.Bollag, G.

(2004) Mol Cell 15: 279-286

  • DOI: 10.1016/j.molcel.2004.07.005
  • Primary Citation of Related Structures:  
    1T9S, 1T9R, 1TB5, 1TAZ, 1TB7, 1TBF, 1TBB

  • PubMed Abstract: 
  • Phosphodiesterases (PDEs) comprise a family of enzymes that modulate the immune response, inflammation, and memory, among many other functions. There are three types of PDEs: cAMP-specific, cGMP-specific, and dual-specific. Here we describe the mecha ...

    Phosphodiesterases (PDEs) comprise a family of enzymes that modulate the immune response, inflammation, and memory, among many other functions. There are three types of PDEs: cAMP-specific, cGMP-specific, and dual-specific. Here we describe the mechanism of nucleotide selectivity on the basis of high-resolution co-crystal structures of the cAMP-specific PDE4B and PDE4D with AMP, the cGMP-specific PDE5A with GMP, and the apo-structure of the dual-specific PDE1B. These structures show that an invariant glutamine functions as the key specificity determinant by a "glutamine switch" mechanism for recognizing the purine moiety in cAMP or cGMP. The surrounding residues anchor the glutamine residue in different orientations for cAMP and for cGMP. The PDE1B structure shows that in dual-specific PDEs a key histidine residue may enable the invariant glutamine to toggle between cAMP and cGMP. The structural understanding of nucleotide binding enables the design of new PDE inhibitors that may treat diseases in which cyclic nucleotides play a critical role.


    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 phosphodiesteraseA347Homo sapiensMutation(s): 18 
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VIA
Query on VIA

Download CCD File 
A
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
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-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 %)
VIAIC50:  5.099999904632568   nM  BindingDB
VIAIC50:  1   nM  BindingDB
VIAIC50:  1.7999999523162842   nM  BindingDB
VIAIC50:  20   nM  BindingDB
VIAIC50:  0.30000001192092896   nM  BindingDB
VIAIC50:  6.599999904632568   nM  BindingDB
VIAIC50:  5.900000095367432   nM  BindingDB
VIAIC50:  2.200000047683716   nM  BindingDB
VIAIC50:  5.599999904632568   nM  BindingDB
VIAIC50:  3.9000000953674316   nM  BindingDB
VIAIC50:  3.5999999046325684   nM  BindingDB
VIAIC50:  1.600000023841858   nM  BindingDB
VIAIC50:  3   nM  BindingDB
VIAIC50:  53   nM  BindingDB
VIAIC50:  3.5   nM  BindingDB
VIAKi:  1.600000023841858   nM  BindingDB
VIAIC50:  4   nM  BindingDB
VIAIC50:  6   nM  BindingDB
VIAIC50:  75   nM  BindingDB
VIAKi:  1.7999999523162842   nM  BindingDB
VIAKi:  1.899999976158142   nM  BindingDB
VIAIC50:  1.7799999713897705   nM  BindingDB
VIAEC50:  8.699999809265137   nM  BindingDB
VIAKi:  10   nM  BindingDB
VIAIC50:  8.5   nM  BindingDB
VIAIC50:  188   nM  BindingDB
VIAIC50:  11   nM  BindingDB
VIAIC50:  3.700000047683716   nM  BindingDB
VIAEC50:  42   nM  BindingDB
VIAIC50:  2.4000000953674316   nM  BindingDB
VIAIC50:  10   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.097α = 90
b = 76.097β = 90
c = 99.272γ = 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: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance