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


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B353Homo sapiensMutation(s): 3 
Gene Names: DPDE4PDE4B
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
PHAROS:  Q07343
GTEx:  ENSG00000184588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07343
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SK4
Query on SK4

Download Ideal Coordinates CCD File 
B [auth A]4-[(3-methoxyphenyl)amino]-6-(methylsulfonyl)quinoline-3-carboxamide
C18 H17 N3 O4 S
SEAXCOHUTXPNQE-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ARS
Query on ARS

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SK4 PDBBind:  3FRG IC50: 3.98 (nM) from 1 assay(s)
BindingDB:  3FRG IC50: 3.98 (nM) from 1 assay(s)
Binding MOAD:  3FRG IC50: 3.98 (nM) from 1 assay(s)
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description