3GWT

Catalytic domain of human phosphodiesterase 4B2B in complex with a quinoline inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Quinolines as a novel structural class of potent and selective PDE4 inhibitors. Optimisation for inhaled administration.

Woodrow, M.D.Ballantine, S.P.Barker, M.D.Clarke, B.J.Dawson, J.Dean, T.W.Delves, C.J.Evans, B.Gough, S.L.Guntrip, S.B.Holman, S.Holmes, D.S.Kranz, M.Lindvaal, M.K.Lucas, F.S.Neu, M.Ranshaw, L.E.Solanke, Y.E.Somers, D.O.Ward, P.Wiseman, J.O.

(2009) Bioorg.Med.Chem.Lett. 19: 5261-5265

  • DOI: 10.1016/j.bmcl.2009.04.012

  • PubMed Abstract: 
  • Crystallography driven optimisation of a lead derived from similarity searching of the GSK compound collection resulted in the discovery of quinoline-3-carboxamides as highly potent and selective inhibitors of phosphodiesterase 4B. This series has be ...

    Crystallography driven optimisation of a lead derived from similarity searching of the GSK compound collection resulted in the discovery of quinoline-3-carboxamides as highly potent and selective inhibitors of phosphodiesterase 4B. This series has been optimized to GSK256066, a potent PDE4B inhibitor which also inhibits LPS induced production of TNF-alpha from isolated human peripheral blood mononuclear cells with a pIC(50) of 11.1. GSK256066 also has a suitable profile for inhaled dosing.


    Organizational Affiliation

    Immuno-Inflammation CEDD Medicinal Chemistry Dept, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK. michael.d.woodrow@gsk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
A
353Homo sapiensMutation(s): 3 
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ARS
Query on ARS

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Download CCD File 
A
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
066
Query on 066

Download SDF File 
Download CCD File 
A
6-{[3-(dimethylcarbamoyl)phenyl]sulfonyl}-4-[(3-methoxyphenyl)amino]-8-methylquinoline-3-carboxamide
C27 H26 N4 O5 S
JFHROPTYMMSOLG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
066IC50: 7900 nM (86) BINDINGDB
066IC50: 0.00794 nM BINDINGMOAD
66IC50: 0.00794 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.706α = 90.00
b = 94.783β = 90.00
c = 105.995γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-04-01 
  • Released Date: 2010-04-07 
  • Deposition Author(s): Somers, D.O., Neu, M.

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description