p38 kinase Crystal structure in complex with small molecule inhibitor

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.259 

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This is version 1.3 of the entry. See complete history


1,7-Naphthyridine 1-Oxides as Novel Potent and Selective Inhibitors of p38 Mitogen Activated Protein Kinase

Lumeras, W.Vidal, L.Vidal, B.Balague, C.Orellana, A.Maldonado, M.Dominguez, M.Segarra, V.Caturla, F.

(2011) J Med Chem 54: 7899-7910

  • DOI: https://doi.org/10.1021/jm200975u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The design, synthesis, and ability to inhibit p38α MAP kinase by a novel series of naphthyridine N-oxides will be described. Some of these compounds showed a significant reduction in the LPS-induced TNFα production in human whole blood. Structure-activity relationship studies revealed that N-oxide oxygen was essential for activity and was probably a determinant factor for its marked selectivity against other related kinases. After an extensive SAR exercise, several compounds from this series were identified as very potent p38α inhibitors. In vivo efficacy of some derivatives was demonstrated to reduce TNFα levels in an acute murine model of inflammation (ED(50) = 0.5 mg/kg in LPS-induced TNFα production when dosed orally 1.5 h prior to LPS administration). The oral efficacy was further demonstrated in a chronic model of adjuvant arthritis in rats with established disease when administered orally (ED(50) < 1 mg/kg).

  • Organizational Affiliation

    Department of Medicinal Chemistry, Almirall Research Center , Almirall S.A., Ctra. Laureà Miró 408, E-08980 Sant Feliu de Llobregat, Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14359Homo sapiensMutation(s): 0 
Gene Names: MAPK14
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 MIH

Download Ideal Coordinates CCD File 
B [auth A]8-(2,6-dichlorophenyl)-4-(2,4-difluorophenyl)-2-piperidin-4-yl-1,7-naphthyridine 7-oxide
C25 H19 Cl2 F2 N3 O
Binding Affinity Annotations 
IDSourceBinding Affinity
MIH PDBBind:  3MW1 IC50: 0.82 (nM) from 1 assay(s)
BindingDB:  3MW1 IC50: 0.82 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.26α = 90
b = 87.23β = 90
c = 122.81γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-07
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description