2ZB0

Crystal structure of P38 in complex with biphenyl amide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
360Homo sapiensMutation(s): 0 
Gene Names: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A)
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to Gene View: MAPK14
Go to UniProtKB:  Q16539
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GK3
Query on GK3

Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GK3IC50: 1500 nM (100) BINDINGDB
GK3Ki: 240 nM (100) BINDINGDB
GK3Ki: 240 nM BINDINGMOAD
GK3Ki: 240 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.378α = 90.00
b = 85.716β = 90.00
c = 124.661γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description