Crystal Structure of Human p38alpha Complexed With a Triazolopyrimidine compound

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Continued exploration of the triazolopyridine scaffold as a platform for p38 MAP kinase inhibition.

Jerome, K.D.Rucker, P.V.Xing, L.Shieh, H.S.Baldus, J.E.Selness, S.R.Letavic, M.A.Braganza, J.F.McClure, K.F.

(2010) Bioorg Med Chem Lett 20: 469-473

  • DOI: https://doi.org/10.1016/j.bmcl.2009.11.114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structure based drug design, synthesis and structure-activity relationship of a series of C6 sulfur linked triazolopyridine based p38 inhibitors are described. The metabolic deficiencies of this series were overcome through changes in the C6 linker from sulfur to methylene, which was predicted by molecular modeling to be bioisosteric. X-ray of the ethylene linked compound 61 confirmed the predicted binding orientation of the scaffold in the p38 enzyme.

  • Organizational Affiliation

    Pfizer Global Research and Development, St. Louis Laboratories, 700 Chesterfield Pkwy. W., Chesterfield, MO 63017, USA. kevin.d.jerome@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo 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 L9G

Download Ideal Coordinates CCD File 
B [auth A]3-{6-[2-(2,4-difluorophenyl)ethyl][1,2,4]triazolo[4,3-a]pyridin-3-yl}-4-methylbenzamide
C22 H18 F2 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
L9G PDBBind:  3KF7 IC50: 40 (nM) from 1 assay(s)
Binding MOAD:  3KF7 IC50: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.068α = 90
b = 74.329β = 90
c = 77.617γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations