3O56

Catalytic domain of human phosphodiesterase 4b2b in complex with a 5-heterocycle pyrazolopyridine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report



Literature

Pyrazolopyridines as potent PDE4B inhibitors: 5-heterocycle SAR.

Mitchell, C.J.Ballantine, S.P.Coe, D.M.Cook, C.M.Delves, C.J.Dowle, M.D.Edlin, C.D.Hamblin, J.N.Holman, S.Johnson, M.R.Jones, P.S.Keeling, S.E.Kranz, M.Lindvall, M.Lucas, F.S.Neu, M.Solanke, Y.E.Somers, D.O.Trivedi, N.A.Wiseman, J.O.

(2010) Bioorg Med Chem Lett 20: 5803-5806

  • DOI: 10.1016/j.bmcl.2010.07.136
  • Primary Citation of Related Structures:  
    3O56, 3O57

  • PubMed Abstract: 
  • Following the discovery of 4-(substituted amino)-1-alkyl-pyrazolo[3,4-b]pyridine-5-carboxamides as potent and selective phosphodiesterase 4B inhibitors, [Hamblin, J. N.; Angell, T.; Ballentine, S., et al. Bioorg. Med. Chem. Lett.2008, 18, 4237] the SAR o ...

    Following the discovery of 4-(substituted amino)-1-alkyl-pyrazolo[3,4-b]pyridine-5-carboxamides as potent and selective phosphodiesterase 4B inhibitors, [Hamblin, J. N.; Angell, T.; Ballentine, S., et al. Bioorg. Med. Chem. Lett.2008, 18, 4237] the SAR of the 5-position was investigated further. A range of substituted heterocycles showed good potencies against PDE4. Optimisation using X-ray crystallography and computational modelling led to the discovery of 16, with sub-nM inhibition of LPS-induced TNF-α production from isolated human peripheral blood mononuclear cells.


    Organizational Affiliation

    GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom. charlotte.j.mitchell@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B A353Homo sapiensMutation(s): 3 
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZG1
Query on ZG1

Download Ideal Coordinates CCD File 
A
1-ethyl-5-[3-(2-oxo-2-pyrrolidin-1-ylethyl)-1,2,4-oxadiazol-5-yl]-N-(tetrahydro-2H-pyran-4-yl)-1H-pyrazolo[3,4-b]pyridin-4-amine
C21 H27 N7 O3
WVSSDMGQAQMULY-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ARS
Query on ARS

Download Ideal Coordinates CCD File 
A
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZG1Kd :  0.7940000295639038   nM  PDBBind
ZG1IC50:  0.7940000295639038   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.531α = 90
b = 94.592β = 90
c = 105.089γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-07-28 
  • Released Date: 2011-08-03 
  • Deposition Author(s): Somers, D.O., Neu, M.

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release