1YW2 | pdb_00001yw2

Mutated Mus Musculus P38 Kinase (mP38)

• PDB DOI: https://doi.org/10.2210/pdb1YW2/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-02-16 Released: 2005-05-10 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.290 (Depositor) 
• R-Value Work: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

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

• PubMed: 15837333 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.72 kDa 
• Atom Count: 2,980 
• Modelled Residue Count: 341 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Mus musculus	Mutation(s): 2  Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811  Go to UniProtKB:  P47811

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGJ	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
ID	Source	Binding Affinity
PGJ	BindingDB:  1YW2	IC50: 460 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.290 (Depositor) 
• R-Value Work:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.036	α = 90
b = 76.954	β = 90
c = 73.637	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-10 
Deposition Author(s): 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.

Revision History  

• 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