3MW1

p38 kinase Crystal structure in complex with small molecule inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.259 

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Literature

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: 10.1021/jm200975u
  • Primary Citation of Related Structures:  
    3MW1

  • 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 ...

    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).

    Related Citations: 
    • Design, synthesis, and structure-activity relationships of aminopyridine N-oxides, a novel scaffold for the potent and selective inhibition of p38 mitogen activated protein kinase
      Lumeras, W., Caturla, J.-F., Vidal, L., Esteve, C., Balague, C., Orellana, A., Dominguez, M., Roca, R., Huerta, J.M., Godessart, N., Vidal, B.
      (2009) J Med Chem 52: 5531
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A359Homo sapiensMutation(s): 0 
Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A
EC: 2.7.11.24
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MIH
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
WLMGLORLNFEUDG-UHFFFAOYSA-N		 Ligand Interaction
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

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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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