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

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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This is version 1.2 of the entry. See complete history


Part 2: Structure-activity relationship (SAR) investigations of fused pyrazoles as potent, selective and orally available inhibitors of p38alpha mitogen-activated protein kinase.

Wurz, R.P.Pettus, L.H.Henkle, B.Sherman, L.Plant, M.Miner, K.McBride, H.J.Wong, L.M.Saris, C.J.Lee, M.R.Chmait, S.Mohr, C.Hsieh, F.Tasker, A.S.

(2010) Bioorg Med Chem Lett 20: 1680-1684

  • DOI: https://doi.org/10.1016/j.bmcl.2010.01.059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel class of pyrazolopyridazine p38alpha mitogen-activated protein kinase (MAPK) inhibitors is disclosed. A structure activity relationship (SAR) investigation was conducted driven by the ability of these compounds to inhibit the p38alpha enzyme, the secretion of TNFalpha in a LPS-challenged THP1 cell line and TNFalpha-induced production of IL-8 in the presence of 50% human whole blood (hWB). This study resulted in the discovery of several inhibitors with IC(50) values in the single-digit nanomolar range in hWB. Further investigation of the pharmacokinetic profiles of these lead compounds led to the identification of three potent and orally bioavailable p38alpha inhibitors 2h, 2m, and 13h. Inhibitor 2m was found to be highly selective for p38alpha/beta over a panel of 402 other kinases in Ambit screening, and was highly efficacious in vivo in the inhibition of TNFalpha production in LPS-stimulated Lewis rats with an ED(50) of ca. 0.08mg/kg.

  • Organizational Affiliation

    Department of Chemistry Research & Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA. rwurz@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 P66

Download Ideal Coordinates CCD File 
B [auth A]4-chloro-N-cyclopropyl-3-{[1-(2,6-difluorophenyl)-1H-pyrazolo[3,4-d]pyridazin-4-yl]amino}benzamide
C21 H15 Cl F2 N6 O
Binding Affinity Annotations 
IDSourceBinding Affinity
P66 BindingDB:  3ITZ Ki: 1 (nM) from 1 assay(s)
IC50: min: 1.4, max: 4 (nM) from 2 assay(s)
PDBBind:  3ITZ IC50: 1.4 (nM) from 1 assay(s)
Binding MOAD:  3ITZ IC50: 1.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.245α = 90
b = 87.847β = 90
c = 121.258γ = 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: 2010-03-02
    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