1YWR

Crystal Structure Analysis of inactive P38 kinase domain in complex with a Monocyclic Pyrazolone Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1YWR/pdb

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


• Deposited: 2005-02-18 Released: 2005-05-10 
• Deposition Author(s): Golebiowski, A., Townes, J.A., Laufersweiler, M.J., Brugel, T.A., Clark, M.P., Clark, C.M., Djung, J.F., Laughlin, S.K., Sabat, M.P., Bookland, R.G., Vanrens, J.C., De, B., Hsieh, L.C., Janusz, M.J., Walter, R.L., Webster, M.E., Mekel, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å

Literature

The development of monocyclic pyrazolone based cytokine synthesis inhibitors.

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

(2005) Bioorg Med Chem Lett 15: 2285-2289

• PubMed: 15837310 
• DOI: https://doi.org/10.1016/j.bmcl.2005.03.007
• Primary Citation of Related Structures:  
  1YWR


• PubMed Abstract: 
  

  4-Aryl-5-pyrimidyl based cytokine synthesis inhibitors that contain a novel monocyclic, pyrazolone heterocyclic core are described. Many of these inhibitors showed low nanomolar activity against LPS-induced TNF-alpha production. One of the compounds (6e) was found to be efficacious in the rat iodoacetate (RIA) in vivo model of osteoarthritis. The X-ray crystal structure of a pyrazolone inhibitor cocrystallized with mutated p38 (mp38) is presented.

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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: 41.79 kDa 
• Atom Count: 2,959 
• Modelled Residue Count: 338 
• 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
LI9	B [auth A]	4-(4-FLUOROPHENYL)-1-METHYL-5-(2-{[(1S)-1-PHENYLETHYL]AMINO}PYRIMIDIN-4-YL)-2-PIPERIDIN-4-YL-1,2-DIHYDRO-3H-PYRAZOL-3-ONE C27 H29 F N6 O OYTOWRNFVUUVHK-SFHVURJKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LI9	PDBBind:  1YWR	IC50: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.736	α = 90
b = 74.575	β = 90
c = 77.377	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345	data collection
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-10 
Deposition Author(s): Golebiowski, A., Townes, J.A., Laufersweiler, M.J., Brugel, T.A., Clark, M.P., Clark, C.M., Djung, J.F., Laughlin, S.K., Sabat, M.P., Bookland, R.G., Vanrens, J.C., De, B., Hsieh, L.C., Janusz, M.J., Walter, R.L., Webster, M.E., Mekel, 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: 2024-02-14
  Changes: Data collection