3FRG

Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with a Quinoline Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Quinolines as a novel structural class of potent and selective PDE4 inhibitors: optimisation for oral administration.

Lunniss, C.J., Cooper, A.W., Eldred, C.D., Kranz, M., Lindvall, M., Lucas, F.S., Neu, M., Preston, A.G., Ranshaw, L.E., Redgrave, A.J., Ed Robinson, J., Shipley, T.J., Solanke, Y.E., Somers, D.O., Wiseman, J.O.

(2009) Bioorg Med Chem Lett 19: 1380-1385

  • DOI: 10.1016/j.bmcl.2009.01.045
  • Primary Citation of Related Structures:  
    3FRG

  • PubMed Abstract: 

    • Crystallography-driven optimisation of a lead derived from similarity searching of the GSK compound collection resulted in the discovery of a series of quinoline derivatives that were highly potent and selective inhibitors of PDE4 with a good pharmacokin ...

    Crystallography-driven optimisation of a lead derived from similarity searching of the GSK compound collection resulted in the discovery of a series of quinoline derivatives that were highly potent and selective inhibitors of PDE4 with a good pharmacokinetic profile in the rat. Quinolines 43 and 48 have potential as oral medicines for the treatment of COPD.

    Organizational Affiliation: 

    GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, England.



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: DPDE4, PDE4B
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
GTEx:  ENSG00000184588
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SK4
Query on SK4
Download Ideal Coordinates CCD File 
A
4-[(3-methoxyphenyl)amino]-6-(methylsulfonyl)quinoline-3-carboxamide
C18 H17 N3 O4 S
SEAXCOHUTXPNQE-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 %)
SK4IC50:  4   nM  Binding MOAD
SK4IC50 :  3.9800000190734863   nM  PDBBind
SK4IC50:  3.9800000190734863   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.485α = 90
b = 94.831β = 90
c = 105.32γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-01-08 
  • Released Date: 2010-01-12 
    • Deposition Author(s): Somers, D.O., Neu, M.

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance