1OUY

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


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 binding of the more specific molecules is characterized by a peptide flip between Met109 and Gly110 ...

    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: 
    • p38MAP kinase inhibitors part 1: Design and development of a new class of potent and highly selective inhibitors based on 3,4-dihydropyrido[3,2-d]pyrimidone scaffold
      Natarajan, S.R., Wisnoski, D.D., Singh, S.B., Stelmach, J.E., O'Neill, E.A., Schwartz, C.D., Thompson, C.M., Fitzgerald, C.E., O'keefe, S.J., Kumar, S., Hop, C.E., Zaller, D.M., Schmatz, D.M., Doherty, J.B.
      (2003) Bioorg Med Chem Lett 13: 273
    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 14 A366Homo sapiensMutation(s): 0 
Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A
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
GTEx:  ENSG00000112062
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
094
Query on 094
Download Ideal Coordinates CCD File 
A
1-(2,6-DICHLOROPHENYL)-6-[(2,4-DIFLUOROPHENYL)SULFANYL]-7-(1,2,3,6-TETRAHYDRO-4-PYRIDINYL)-3,4-DIHYDROPYRIDO[3,2-D]PYRIMIDIN-2(1H)-ONE
C24 H18 Cl2 F2 N4 O S
PZUXNWPJBLCJKB-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
094IC50:  160   nM  BindingDB
94IC50 :  4.300000190734863   nM  PDBBind
094IC50:  4.300000190734863   nM  BindingDB
094IC50:  61   nM  BindingDB
094IC50:  4.300000190734863   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
CNSphasing

Structure Validation

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View more in-depth experimental data

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