Crystal Structure of p38a Mitogen-Activated Protein Kinase in Complex with a Pyrazolopyridinone Inhibitor.

Experimental Data Snapshot

  • Resolution: 3.31 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

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This is version 1.2 of the entry. See complete history


Discovery and evaluation of 7-alkyl-1,5-bis-aryl-pyrazolopyridinones as highly potent, selective, and orally efficacious inhibitors of p38alpha mitogen-activated protein kinase.

Pettus, L.H.Wurz, R.P.Xu, S.Herberich, B.Henkle, B.Liu, Q.McBride, H.J.Mu, S.Plant, M.H.Saris, C.J.Sherman, L.Wong, L.M.Chmait, S.Lee, M.R.Mohr, C.Hsieh, F.Tasker, A.S.

(2010) J Med Chem 53: 2973-2985

  • DOI: https://doi.org/10.1021/jm100095x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The p38alpha mitogen-activated protein (MAP) kinase is a central signaling molecule in many proinflammatory pathways, regulating the cellular response to a multitude of external stimuli including heat, ultraviolet radiation, osmotic shock, and a variety of cytokines especially interleukin-1beta and tumor necrosis factor alpha. Thus, inhibitors of this enzyme are postulated to have significant therapeutic potential for the treatment of rheumatoid arthritis, inflammatory bowel disease, and Crohn's disease, as well as other diseases where aberrant cytokine signaling is the driver of disease. In this communication, we describe a novel class of 7-alkyl-1,5-bis-aryl-pyrazolopyridinone-based p38alpha inhibitors. In particular, compound 3f is highly potent in the enzyme and cell-based assays, selective in an Ambit kinase screen, and efficacious (ED(50) < or = 0.01 mg/kg) in the rat collagen induced arthritis (CIA) model.

  • Organizational Affiliation

    Departments of Chemistry Research and Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, USA. lpettus@amgen.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14366Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LHJ

Download Ideal Coordinates CCD File 
B [auth A]N-cyclopropyl-3-[1-(2,4-difluorophenyl)-7-methyl-6-oxo-6,7-dihydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-4-methylbenzamide
C24 H20 F2 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
LHJ BindingDB:  3LHJ Ki: 2.3 (nM) from 1 assay(s)
Kd: min: 0.3, max: 0.31 (nM) from 2 assay(s)
PDBBind:  3LHJ Kd: 0.31 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.31 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.775α = 90
b = 86.604β = 90
c = 118.959γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations