Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.52 kDa 
• Atom Count: 2913 
• Residue Count: 350 
• Unique protein chains: 1

1OUY

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

• DOI: 10.2210/pdb1OUY/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-03-25 Released: 2003-09-02 
• Deposition Author(s): Fitzgerald, C.E., Patel, S.B., Becker, J.W., Cameron, P.M., Zaller, D., Pikounis, V.B., O'Keefe, S.J., Scapin, G.

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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 

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

• PubMed: 12897767 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	366	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
094	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
094	IC50:  160   nM  BindingDB
94	IC50 :  4.300000190734863   nM  PDBBind
094	IC50:  4.300000190734863   nM  BindingDB
094	IC50:  61   nM  BindingDB
094	IC50:  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 = 45.63	α = 90
b = 86.764	β = 90
c = 126.398	γ = 90

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-25 
• Released Date: 2003-09-02 
Deposition Author(s): Fitzgerald, C.E., Patel, S.B., Becker, J.W., Cameron, P.M., Zaller, D., Pikounis, V.B., O'Keefe, S.J., Scapin, G.

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