1OVE

The structure of p38 alpha in complex with a dihydroquinolinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for p38alpha MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificity

Fitzgerald, C.E.Patel, S.B.Becker, J.W.Cameron, P.M.Zaller, D.Pikounis, V.B.O'Keefe, S.J.Scapin, G.

(2003) Nat Struct Biol 10: 764-769

  • DOI: 10.1038/nsb949
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The quinazolinone and pyridol-pyrimidine classes of p38 MAP kinase inhibitors have a previously unseen degree of specificity for p38 over other MAP kinases. Comparison of the crystal structures of p38 bound to four different compounds shows that bind ...

    The quinazolinone and pyridol-pyrimidine classes of p38 MAP kinase inhibitors have a previously unseen degree of specificity for p38 over other MAP kinases. Comparison of the crystal structures of p38 bound to four different compounds shows that binding of the more specific molecules is characterized by a peptide flip between Met109 and Gly110. Gly110 is a residue specific to the alpha, beta and gamma isoforms of p38. The delta isoform and the other MAP kinases have bulkier residues in this position. These residues would likely make the peptide flip energetically unfavorable, thus explaining the selectivity of binding. To test this hypothesis, we constructed G110A and G110D mutants of p38 and measured the potency of several compounds against them. The results confirm that the selectivity of quinazolinones and pyridol-pyrimidines results from the presence of a glycine in position 110. This unique mode of binding may be exploited in the design of new p38 inhibitors.


    Related Citations: 
    • Design and synthesis of potent, orally bioavailable dihydroquinazolinone inhibitors of p38 MAP kinase
      Stelmach, J.E., Liu, L., Patel, S.B., Pivnichny, J.V., Scapin, G., Singh, S., Hop, C.E., Wang, Z., Cameron, P.M., Nichols, E.A., O'Keefe, S.J., O'Neill, E.A., Schmatz, D.M., Schwartz, C.D., Thompson, C.M., Zaller, D.M., Doherty, J.B.
      (2003) Bioorg Med Chem Lett 13: 277

    Organizational Affiliation

    Department of Immunology, Merck Research Laboratories, PO Box 2000, Rahway, New Jersey 07065, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14A366Homo sapiensMutation(s): 1 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
358
Query on 358

Download CCD File 
A
1-(2,6-DICHLOROPHENYL)-5-(2,4-DIFLUOROPHENYL)-7-PIPERIDIN-4-YL-3,4-DIHYDROQUINOLIN-2(1H)-ONE
C26 H22 Cl2 F2 N2 O
VXIYTVJEIXMAQF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
358IC50:  14   nM  BindingDB
358IC50:  0.7400000095367432   nM  Binding MOAD
358IC50 :  0.7400000095367432   nM  PDBBind
358IC50:  0.7400000095367432   nM  BindingDB
358IC50:  6.400000095367432   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.009α = 90
b = 87.1β = 90
c = 122.613γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance