1XMY

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R)-Rolipram


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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
cAMP-specific 3',5'-cyclic phosphodiesterase 4BA398Homo 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4BB398Homo 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
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROL
Query on ROL

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

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

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4RRKi:  11   nM  BindingDB
4RRIC50:  1100   nM  BindingDB
4RRIC50:  1220   nM  BindingDB
4RRKi:  1470   nM  BindingDB
4RRIC50:  1000   nM  BindingDB
4RRIC50:  2000   nM  BindingDB
4RRIC50:  941   nM  BindingDB
4RRIC50:  2700   nM  BindingDB
4RRIC50:  105   nM  BindingDB
4RRIC50:  1500   nM  BindingDB
4RRIC50:  98   nM  BindingDB
4RRIC50:  100   nM  BindingDB
4RRIC50:  86   nM  BindingDB
4RREC50:  220   nM  BindingDB
4RRKi:  4100   nM  BindingDB
4RRIC50:  80   nM  BindingDB
4RRIC50:  1270   nM  BindingDB
4RRIC50:  1300   nM  BindingDB
4RRIC50:  498   nM  BindingDB
4RRIC50:  34   nM  BindingDB
4RRKi:  16.600000381469727   nM  BindingDB
4RRIC50:  52   nM  BindingDB
4RRIC50:  741   nM  BindingDB
4RRIC50:  50   nM  BindingDB
ROLIC50 :  50.119998931884766   nM  PDBBind
4RRIC50:  625   nM  BindingDB
4RRIC50:  4000   nM  BindingDB
4RRIC50:  231   nM  BindingDB
4RRIC50:  740   nM  BindingDB
4RRIC50:  35.70000076293945   nM  BindingDB
ROLIC50:  570   nM  Binding MOAD
4RRIC50:  20   nM  BindingDB
4RRIC50:  2000   nM  BindingDB
4RRIC50:  4   nM  BindingDB
4RRIC50:  1900   nM  BindingDB
4RRIC50:  1120   nM  BindingDB
4RRIC50:  1800   nM  BindingDB
4RRIC50:  570   nM  BindingDB
4RRIC50:  210   nM  BindingDB
4RRIC50:  6   nM  BindingDB
4RRKi:  220   nM  BindingDB
4RRKi:  221   nM  BindingDB
4RRKi:  224   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.67α = 90
b = 94.633β = 90
c = 106.432γ = 90
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