3D7Z

Crystal Structure of P38 Kinase in Complex with a biphenyl amide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 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 3: Improvement of cellular and in vivo activity.

Angell, R.Aston, N.M.Bamborough, P.Buckton, J.B.Cockerill, S.deBoeck, S.J.Edwards, C.D.Holmes, D.S.Jones, K.L.Laine, D.I.Patel, S.Smee, P.A.Smith, K.J.Somers, D.O.Walker, A.L.

(2008) Bioorg.Med.Chem.Lett. 18: 4428-4432

  • DOI: 10.1016/j.bmcl.2008.06.048

  • PubMed Abstract: 
  • The biphenyl amides (BPAs) are a novel series of p38alpha MAP kinase inhibitor. The optimisation of the series to give compounds that are potent in an in vivo disease model is discussed. SAR is presented and rationalised with reference to the crystal ...

    The biphenyl amides (BPAs) are a novel series of p38alpha MAP kinase inhibitor. The optimisation of the series to give compounds that are potent in an in vivo disease model is discussed. SAR is presented and rationalised with reference to the crystallographic binding mode.


    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 sapiensGene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GK5
Query on GK5

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Download CCD File 
A
N~3~-cyclopropyl-N~4~'-(cyclopropylmethyl)-6-methylbiphenyl-3,4'-dicarboxamide
N3-cyclopropyl-N4'-(cyclopropylmethyl)-6-methyl-3,4'-biphenyldicarboxamide
C22 H24 N2 O2
BOPSUAHGQHFKGG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GK5Ki: 9 - 12.6 nM (100) BINDINGDB
GK5IC50: 18 - 1584.9 nM (100) BINDINGDB
GK5Ki: 12 nM BINDINGMOAD
GK5Ki: 12 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.630α = 90.00
b = 86.103β = 90.00
c = 124.811γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description