p38 kinase crystal structure in complex with small molecule inhibitor

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Novel triazolopyridylbenzamides as potent and selective p38 alpha inhibitors.

Aiguade, J.Balague, C.Carranco, I.Caturla, F.Dominguez, M.Eastwood, P.Esteve, C.Gonzalez, J.Lumeras, W.Orellana, A.Preciado, S.Roca, R.Vidal, L.Vidal, B.

(2012) Bioorg Med Chem Lett 22: 3431-3436

  • DOI: https://doi.org/10.1016/j.bmcl.2012.03.099
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A new class of p38α inhibitors based on a biaryl-triazolopyridine scaffold was investigated. X-ray crystallographic data of the initial lead compound cocrystallised with p38α was crucial in order to uncover a unique binding mode of the inhibitor to the hinge region via a pair of water molecules. Synthesis and SAR was directed towards the improvement of binding affinity, as well as ADME properties for this new class of p38α inhibitors and ultimately afforded compounds showing good in vivo efficacy.

  • Organizational Affiliation

    Almirall Research Center, Almirall SA, Ctra. Laureà Miró 408, E-08980 Sant, Feliu de Llobregat, Barcelona, Spain. josep.aiguade@almirall.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14349Homo 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 CQ0

Download Ideal Coordinates CCD File 
B [auth A]3-(3-tert-butyl[1,2,4]triazolo[4,3-a]pyridin-7-yl)-N-cyclopropyl-4-methylbenzamide
C21 H24 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
CQ0 PDBBind:  3S3I IC50: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.28α = 90
b = 84.96β = 90
c = 123.51γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description