1YWR

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


Experimental Data Snapshot

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

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A360Mus musculusMutation(s): 2 
Gene Names: Mapk14Crk1Csbp1Csbp2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47811
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LI9
Query on LI9

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LI9 PDBBind:  1YWR IC50: 13 (nM) from 1 assay(s)
Binding MOAD:  1YWR IC50: 32 (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 = 65.736α = 90
b = 74.575β = 90
c = 77.377γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

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