1OUK

The structure of p38 alpha in complex with a pyridinylimidazole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    1OUK, 1OUY, 1OVE

  • 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, selective, and orally bioavailable tetrasubstituted imidazole inhibitors of p38 mitogen-activated protein kinase
      Liverton, N.J., Butcher, J.W., Claiborne, C.F., Claremon, D.A., Libby, B.E., Nguyen, K.T., Pitzenberger, S.M., Selnick, H.G., Smith, G.R., Tebben, A., Vacca, J.P., Varga, S.L., Agarwal, L., Dancheck, K., Forsyth, A.J., Fletcher, D.S., Frantz, B., Hanlon, W.A., Harper, C.F., Hofsess, S.J., Kostura, M., Lin, J., Luell, S., O'Neill, E.A., O'Keefe, S.J.
      (1999) J Med Chem 42: 2180

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A366Homo sapiensMutation(s): 0 
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
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
084
Query on 084

Download CCD File 
A
4-[5-[2-(1-PHENYL-ETHYLAMINO)-PYRIMIDIN-4-YL]-1-METHYL-4-(3-TRIFLUOROMETHYLPHENYL)-1H-IMIDAZOL-2-YL]-PIPERIDINE
C28 H29 F3 N6
QICPQLFMWYQJGX-SFHVURJKSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
084IC50:  0.10000000149011612   nM  BindingDB
84IC50 :  0.12999999523162842   nM  PDBBind
084IC50:  110   nM  BindingDB
084IC50:  0.12999999523162842   nM  BindingDB
084IC50:  0.10999999940395355   nM  BindingDB
084IC50:  0.14000000059604645   nM  BindingDB
084IC50:  0.12999999523162842   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.702α = 90
b = 88.038β = 90
c = 126.047γ = 90
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction
CNSrefinement
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: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description