2GHM | pdb_00002ghm

Mutated MAP kinase P38 (Mus Musculus) in complex with Inhbitor PG-895449

• PDB DOI: https://doi.org/10.2210/pdb2GHM/pdb

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


• Deposited: 2006-03-27 Released: 2006-05-02 
• Deposition Author(s): Walter, R.L., Mekel, M.J., Evdokimov, A.G., Pokross, M.E., Maier, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.323 (Depositor) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

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

• PubMed: 16632356 
• DOI: https://doi.org/10.1016/j.bmcl.2006.03.095
• Primary Citation of Related Structures:  
  2GHL, 2GHM


• 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-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.

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Organizational Affiliation: 

Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd., Mason, OH 45040, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.32 kDa 
• Atom Count: 2,867 
• Modelled Residue Count: 336 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	348	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
LIC	B [auth A]	3-(2-CHLOROBENZYL)-1-(2-{[(1S)-2-HYDROXY-1,2-DIMETHYLPROPYL]AMINO}PYRIMIDIN-4-YL)-1-(4-METHOXYPHENYL)UREA C24 H28 Cl N5 O3 ZHBOBAJCKHPQBT-INIZCTEOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.323 (Depositor) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.169	α = 90
b = 74.855	β = 90
c = 77.879	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-02 
Deposition Author(s): Walter, R.L., Mekel, M.J., Evdokimov, A.G., Pokross, M.E., Maier, J.A.

Revision History  

• Version 1.0: 2006-05-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-14
  Changes: Data collection