1RO6

Crystal structure of PDE4B2B complexed with Rolipram (R & S)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the catalytic domain of phosphodiesterase 4B complexed with AMP, 8-Br-AMP, and rolipram.

Xu, R.X.Rocque, W.J.Lambert, M.H.Vanderwall, D.E.Luther, M.A.Nolte, R.T.

(2004) J Mol Biol 337: 355-365

  • DOI: 10.1016/j.jmb.2004.01.040
  • Primary Citation of Related Structures:  
    1RO9, 1RO6, 1ROR

  • PubMed Abstract: 
  • Phosphodiesterase catalyzes the hydrolysis of the intracellular second messenger 3',5'-cyclic AMP (cAMP) into the corresponding 5'-nucleotide. Phosphodiesterase 4 (PDE4), the major cAMP-specific PDE in inflammatory and immune cells, is an attractive targ ...

    Phosphodiesterase catalyzes the hydrolysis of the intracellular second messenger 3',5'-cyclic AMP (cAMP) into the corresponding 5'-nucleotide. Phosphodiesterase 4 (PDE4), the major cAMP-specific PDE in inflammatory and immune cells, is an attractive target for the treatment of asthma and COPD. We have determined crystal structures of the catalytic domain of PDE4B complexed with AMP (2.0 A), 8-Br-AMP (2.13 A) and the potent inhibitor rolipram (2.0 A). All the ligands bind in the same hydrophobic pocket and can interact directly with the active site metal ions. The identity of these metal ions was examined using X-ray anomalous difference data. The structure of the AMP complex confirms the location of the catalytic site and allowed us to speculate about the detailed mechanism of catalysis. The high-resolution structures provided the experimental insight into the nucleotide selectivity of phosphodiesterase. 8-Br-AMP binds in the syn conformation to the enzyme and demonstrates an alternative nucleotide-binding mode. Rolipram occupies much of the AMP-binding site and forms two hydrogen bonds with Gln443 similar to the nucleotides.


    Organizational Affiliation

    Department of Computational, Analytical and Structural Sciences, GlaxoSmithKline, 5 Moore Drive, V-180, Research Triangle Park, NC 27709, USA. robert.x.xu@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B AB378Homo sapiensMutation(s): 2 
Gene Names: PDE4BDPDE4
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
NIH Common Fund Data Resources
PHAROS:  Q07343
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4RRIC50:  3450   nM  BindingDB
4RRIC50:  3500   nM  BindingDB
4RRIC50:  4000   nM  BindingDB
4RRIC50:  4750   nM  BindingDB
4RRIC50:  20   nM  BindingDB
4RRIC50:  5000   nM  BindingDB
4RRIC50:  35.70000076293945   nM  BindingDB
4RRIC50:  25   nM  BindingDB
4RRIC50:  34   nM  BindingDB
4RRIC50:  52   nM  BindingDB
4RRIC50:  50   nM  BindingDB
4RRKi:  4100   nM  BindingDB
4RRKi:  4.5   nM  BindingDB
4RRKi:  1470   nM  BindingDB
4RRKi:  11   nM  BindingDB
4RRIC50:  80   nM  BindingDB
4RRIC50:  86   nM  BindingDB
4RRIC50:  98   nM  BindingDB
4RRIC50:  105   nM  BindingDB
4RRIC50:  100   nM  BindingDB
ROLKi:  375   nM  Binding MOAD
4RRIC50:  210   nM  BindingDB
4RRIC50:  231   nM  BindingDB
4RRIC50:  320   nM  BindingDB
4RRKi:  16.600000381469727   nM  BindingDB
4RRIC50:  400   nM  BindingDB
4RRIC50:  740   nM  BindingDB
4RRKi:  1.600000023841858   nM  BindingDB
4RRIC50:  498   nM  BindingDB
4RRIC50:  500   nM  BindingDB
4RRIC50:  570   nM  BindingDB
4RRIC50:  550   nM  BindingDB
4RRIC50:  625   nM  BindingDB
4RRKi:  1000   nM  BindingDB
4RRIC50:  741   nM  BindingDB
4RRIC50:  2700   nM  BindingDB
4RREC50:  220   nM  BindingDB
4RRIC50:  930   nM  BindingDB
4RRIC50:  941   nM  BindingDB
4RRIC50:  1000   nM  BindingDB
4RRIC50:  1100   nM  BindingDB
4RRIC50:  2000   nM  BindingDB
4RRIC50:  1270   nM  BindingDB
4RRIC50:  1300   nM  BindingDB
4RRIC50:  1220   nM  BindingDB
4RRIC50:  1500   nM  BindingDB
4RRIC50:  1680   nM  BindingDB
4RRIC50:  1600   nM  BindingDB
4RRIC50:  1800   nM  BindingDB
4RRIC50:  1900   nM  BindingDB
4RRKi:  3.799999952316284   nM  BindingDB
4RRIC50:  1120   nM  BindingDB
4RRIC50:  2000   nM  BindingDB
4RRIC50:  4   nM  BindingDB
4RRKi:  220   nM  BindingDB
4RRKi:  221   nM  BindingDB
4RRKi:  224   nM  BindingDB
ROLKi :  350   nM  PDBBind
4RRIC50:  6   nM  BindingDB
4RRIC50:  3340   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.148α = 90
b = 160.891β = 90
c = 108.78γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance