1Q9M

Three dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Three dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity

Huai, Q.Wang, H.Sun, Y.Kim, H.Y.Liu, Y.Ke, H.

(2003) Structure 11: 865-873

  • DOI: 10.1016/s0969-2126(03)00123-0
  • Primary Citation of Related Structures:  
    1Q9M, 1OYN

  • PubMed Abstract: 
  • Selective inhibitors against the 11 families of cyclic nucleotide phosphodiesterases (PDEs) are used to treat various human diseases. How the inhibitors selectively bind the conserved PDE catalytic domains is unknown. The crystal structures of the PD ...

    Selective inhibitors against the 11 families of cyclic nucleotide phosphodiesterases (PDEs) are used to treat various human diseases. How the inhibitors selectively bind the conserved PDE catalytic domains is unknown. The crystal structures of the PDE4D2 catalytic domain in complex with (R)- or (R,S)-rolipram suggest that inhibitor selectivity is determined by the chemical nature of amino acids and subtle conformational changes of the binding pockets. The conformational states of Gln369 in PDE4D2 may play a key role in inhibitor recognition. The corresponding Y329S mutation in PDE7 may lead to loss of the hydrogen bonds between rolipram and Gln369 and is thus a possible reason explaining PDE7's insensitivity to rolipram inhibition. Docking of the PDE5 inhibitor sildenafil into the PDE4 catalytic pocket further helps understand inhibitor selectivity.


    Organizational Affiliation

    Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific phosphodiesterase PDE4D2ABCD360Homo sapiensMutation(s): 0 
Gene Names: PDE4DDPDE3
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
Find proteins for Q08499 (Homo sapiens)
Explore Q08499 
Go to UniProtKB:  Q08499
NIH Common Fund Data Resources
PHAROS  Q08499
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROL
Query on ROL

Download CCD File 
A, B, C, D
ROLIPRAM
C16 H21 N O3
HJORMJIFDVBMOB-LBPRGKRZSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4RRIC50:  33   nM  BindingDB
4RRIC50:  41   nM  BindingDB
4RRIC50:  50   nM  BindingDB
4RRIC50:  13000   nM  BindingDB
4RRKi:  8460   nM  BindingDB
4RRIC50:  6500   nM  BindingDB
4RRIC50:  130   nM  BindingDB
4RRKi:  4100   nM  BindingDB
4RRIC50:  160   nM  BindingDB
ROLIC50 :  330   nM  PDBBind
4RRIC50:  140   nM  BindingDB
4RRKi:  11   nM  BindingDB
4RRIC50:  60   nM  BindingDB
4RRIC50:  80   nM  BindingDB
4RRIC50:  70   nM  BindingDB
4RRIC50:  17000   nM  BindingDB
4RRIC50:  31.600000381469727   nM  BindingDB
4RRIC50:  92   nM  BindingDB
4RRIC50:  83   nM  BindingDB
4RRIC50:  90   nM  BindingDB
4RRIC50:  600   nM  BindingDB
4RRIC50:  610   nM  BindingDB
4RRIC50:  620   nM  BindingDB
4RRIC50:  622   nM  BindingDB
4RRIC50:  550   nM  BindingDB
4RRIC50:  590   nM  BindingDB
4RRIC50:  1100   nM  BindingDB
4RRKi:  930   nM  BindingDB
4RRIC50:  740   nM  BindingDB
4RRIC50:  910   nM  BindingDB
4RRKi:  16.600000381469727   nM  BindingDB
4RRIC50:  320   nM  BindingDB
4RRKi:  375   nM  BindingDB
4RRKi:  382   nM  BindingDB
4RRKi:  490   nM  BindingDB
4RRIC50:  390   nM  BindingDB
4RRKi:  58.900001525878906   nM  BindingDB
4RREC50:  1100   nM  BindingDB
4RRIC50:  398   nM  BindingDB
4RRIC50:  400   nM  BindingDB
4RRIC50:  2000   nM  BindingDB
4RRIC50:  2000   nM  BindingDB
4RRIC50:  2500   nM  BindingDB
4RRIC50:  3000   nM  BindingDB
4RRIC50:  2800   nM  BindingDB
4RRKi:  300   nM  BindingDB
4RRIC50:  3500   nM  BindingDB
ROLIC50:  330   nM  Binding MOAD
4RRIC50:  2700   nM  BindingDB
4RRIC50:  1000   nM  BindingDB
4RRIC50:  1050   nM  BindingDB
4RRIC50:  1120   nM  BindingDB
4RRIC50:  4   nM  BindingDB
4RRIC50:  1170   nM  BindingDB
4RRIC50:  1430   nM  BindingDB
4RRIC50:  4   nM  BindingDB
4RRIC50:  6   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.272α = 90
b = 112.493β = 90
c = 160.908γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance