2GHL

Mutant Mus Musculus P38 Kinase Domain in Complex with Inhibitor PG-874743


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Development of N-2,4-pyrimidine-N-phenyl-N'-phenyl ureas as inhibitors of tumor necrosis factor alpha (TNF-alpha) synthesis. Part 1.

Brugel, T.A.Maier, J.A.Clark, M.P.Sabat, M.Golebiowski, A.Bookland, R.G.Laufersweiler, M.J.Laughlin, S.K.Vanrens, J.C.De, B.Hsieh, L.C.Mekel, M.J.Janusz, M.J.

(2006) Bioorg.Med.Chem.Lett. 16: 3510-3513

  • DOI: 10.1016/j.bmcl.2006.03.095
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A new class of tumor necrosis factor alpha (TNF-alpha) synthesis inhibitors based on an N-2,4-pyrimidine-N-phenyl-N'-phenyl urea scaffold is described. Many of these compounds showed low-nanomolar activity against lipopolysaccharide stimulated TNF-al ...

    A new class of tumor necrosis factor alpha (TNF-alpha) synthesis inhibitors based on an N-2,4-pyrimidine-N-phenyl-N'-phenyl urea scaffold is described. Many of these compounds showed low-nanomolar activity against lipopolysaccharide stimulated TNF-alpha production. X-ray co-crystallization studies with mutated p38alpha showed that these trisubstituted ureas interact with the ATP-binding pocket in a pseudo-bicyclic conformation brought about by the presence of an intramolecular hydrogen bonding interaction.


    Organizational Affiliation

    Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd., Mason, OH 45040, USA. brugel.ta@pg.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
348Mus musculusMutation(s): 2 
Gene Names: Mapk14 (Crk1, Csbp1, Csbp2)
EC: 2.7.11.24
Find proteins for P47811 (Mus musculus)
Go to UniProtKB:  P47811
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LIB
Query on LIB

Download SDF File 
Download CCD File 
A
3-(2-CHLOROPHENYL)-1-(2-{[(1S)-2-HYDROXY-1,2-DIMETHYLPROPYL]AMINO}PYRIMIDIN-4-YL)-1-(4-METHOXYPHENYL)UREA
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
C23 H26 Cl N5 O3
ZWYFTKPEHRQCCW-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LIBIC50: 92 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.261α = 90.00
b = 74.426β = 90.00
c = 76.938γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MAR345data collection
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description