The structure of p38 alpha in complex with a dihydropyrido-pyrimidine inhibitor

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


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: https://doi.org/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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14366Homo 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 094

Download Ideal Coordinates CCD File 
C24 H18 Cl2 F2 N4 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
094 BindingDB:  1OUY IC50: min: 4.3, max: 160 (nM) from 3 assay(s)
Binding MOAD:  1OUY IC50: 4.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.63α = 90
b = 86.764β = 90
c = 126.398γ = 90
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description