2ZB0

Crystal structure of P38 in complex with biphenyl amide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Biphenyl amide p38 kinase inhibitors 1: Discovery and binding mode

Angell, R.M.Bamborough, P.Cleasby, A.Cockerill, S.G.Jones, K.L.Mooney, C.J.Somers, D.O.Walker, A.L.

(2008) Bioorg Med Chem Lett 18: 318-323

  • DOI: 10.1016/j.bmcl.2007.10.076
  • Primary Citation of Related Structures:  
    2ZB0, 2ZB1, 2ZAZ

  • PubMed Abstract: 
  • The biphenyl amides (BPAs) are a novel series of p38 MAP kinase inhibitors. The discovery of the series through structure-based focused screening is described, and the binding mode of the compounds is explained with reference to X-ray crystal structu ...

    The biphenyl amides (BPAs) are a novel series of p38 MAP kinase inhibitors. The discovery of the series through structure-based focused screening is described, and the binding mode of the compounds is explained with reference to X-ray crystal structures.


    Related Citations: 
    • Biphenyl amide p38 kinase inhibitors 2: Optimisation and SAR
      Angell, R.M., Angell, T.D., Bamborough, P., Brown, D., Brown, M., Buckton, J.B., Cockerill, S.G., Edwards, C.D., Jones, K.L., Longstaff, T., Smee, P.A., Smith, K.J., Somers, D.O., Walker, A.L., Willson, M.
      (2008) Bioorg Med Chem Lett 18: 324

    Organizational Affiliation

    GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A360Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GK3
Query on GK3

Download CCD File 
A
N-(3-cyanophenyl)-2'-methyl-5'-(5-methyl-1,3,4-oxadiazol-2-yl)-4-biphenylcarboxamide
C24 H18 N4 O2
PMMLSQFPBFKLHH-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GK3IC50:  1500   nM  BindingDB
GK3Ki :  240   nM  PDBBind
GK3Ki:  240   nM  Binding MOAD
GK3Ki:  240   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.378α = 90
b = 85.716β = 90
c = 124.661γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-10-13 
  • Released Date: 2008-01-15 
  • Deposition Author(s): Somers, D.O.

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description