1YW2

Mutated Mus Musculus P38 Kinase (mP38)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

The development of new isoxazolone based inhibitors of tumor necrosis factor-alpha (TNF-alpha) production.

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

(2005) Bioorg Med Chem Lett 15: 2399-2403

  • DOI: https://doi.org/10.1016/j.bmcl.2005.02.066
  • Primary Citation of Related Structures:  
    1YW2

  • PubMed Abstract: 

    4-Aryl-3-pyridyl and 4-aryl-3-pyrimidinyl based tumor necrosis factor-alpha (TNF-alpha) inhibitors, which contain a novel isoxazolone five-membered heterocyclic core are described. Many showed sub-micromolar activity against lipopolysaccharide-induced TNF-alpha production.

    • Organizational Affiliation: 

    Health Care Research Center, Procter and Gamble Pharmaceuticals, 8700 Mason-Montgomery Road, Mason, OH 45040, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Mus musculusMutation(s): 2 
Gene Names: Mapk14, Crk1, Csbp1, Csbp2
EC: 2.7.1.37
UniProt
Find proteins for P47811 (Mus musculus)
Explore P47811 
Go to UniProtKB:  P47811
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47811
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGJ
Query on PGJ
Download Ideal Coordinates CCD File 
B [auth A]2-(ETHOXYMETHYL)-4-(4-FLUOROPHENYL)-3-[2-(2-HYDROXYPHENOXY)PYRIMIDIN-4-YL]ISOXAZOL-5(2H)-ONE
C22 H18 F N3 O5
ZSOXFJURLPCSOO-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PGJ PDBBind:  1YW2 IC50: 141 (nM) from 1 assay(s)
BindingDB:  1YW2 IC50: 460 (nM) from 1 assay(s)
Binding MOAD:  1YW2 IC50: 141 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.036α = 90
b = 76.954β = 90
c = 73.637γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description