1RO6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 

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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
A, B
378Homo sapiensMutation(s): 2 
Gene Names: PDE4B (DPDE4)
EC: 3.1.4.53
Find proteins for Q07343 (Homo sapiens)
Go to Gene View: PDE4B
Go to UniProtKB:  Q07343
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ROL
Query on ROL

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Download CCD File 
A, B
ROLIPRAM
(4R)-[3-(CYCLOPENTYLOXY)-4-METHOXYPHENYL]-2-PYRROLIDINONE
C16 H21 N O3
HJORMJIFDVBMOB-LBPRGKRZSA-N
 Ligand Interaction
ARS
Query on ARS

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Download CCD File 
A
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.148α = 90.00
b = 160.891β = 90.00
c = 108.780γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

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