1XMU

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Roflumilast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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): 0 
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4BB398Homo sapiensMutation(s): 0 
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
ROF
Query on ROF

Download CCD File 
A, B
3-(CYCLOPROPYLMETHOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-(DIFLUOROMETHOXY)BENZAMIDE
C17 H14 Cl2 F2 N2 O3
MNDBXUUTURYVHR-UHFFFAOYSA-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 %)
ROFIC50:  0.800000011920929   nM  BindingDB
ROFIC50:  1   nM  BindingDB
ROFKi:  3   nM  BindingDB
ROFIC50:  0.8399999737739563   nM  BindingDB
ROFIC50:  0.49000000953674316   nM  BindingDB
ROFIC50:  1.100000023841858   nM  BindingDB
ROFKi:  0.4000000059604645   nM  BindingDB
ROFIC50:  0.8899999856948853   nM  BindingDB
ROFIC50:  0.8399999737739563   nM  BindingDB
ROFIC50:  0.4000000059604645   nM  BindingDB
ROFIC50:  0.699999988079071   nM  BindingDB
ROFIC50:  0.8999999761581421   nM  BindingDB
ROFKi:  2.4000000953674316   nM  BindingDB
ROFIC50 :  0.8399999737739563   nM  PDBBind
ROFIC50:  0.8399999737739563   nM  Binding MOAD
ROFIC50:  670   nM  BindingDB
ROFIC50:  0.6899999976158142   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.316α = 90
b = 94.1β = 90
c = 108.026γ = 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