P38 Alpha kinase complexed with a 2-aminothiazol-5-yl-pyrimidine based inhibitor

Experimental Data Snapshot

  • Resolution: 2.09 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Utilization of a nitrogen-sulfur nonbonding interaction in the design of new 2-aminothiazol-5-yl-pyrimidines as p38alpha MAP kinase inhibitors.

Lin, S.Wrobleski, S.T.Hynes, J.Pitt, S.Zhang, R.Fan, Y.Doweyko, A.M.Kish, K.F.Sack, J.S.Malley, M.F.Kiefer, S.E.Newitt, J.A.McKinnon, M.Trzaskos, J.Barrish, J.C.Dodd, J.H.Schieven, G.L.Leftheris, K.

(2010) Bioorg Med Chem Lett 20: 5864-5868

  • DOI: https://doi.org/10.1016/j.bmcl.2010.07.102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The design, synthesis, and structure-activity relationships (SAR) of a series of 2-aminothiazol-5-yl-pyrimidines as novel p38α MAP kinase inhibitors are described. These efforts led to the identification of 41 as a potent p38α inhibitor that utilizes a unique nitrogen-sulfur intramolecular nonbonding interaction to stabilize the conformation required for binding to the p38α active site. X-ray crystallographic studies that confirm the proposed binding mode of this class of inhibitors in p38 α and provide evidence for the proposed intramolecular nitrogen-sulfur interaction are discussed.

  • Organizational Affiliation

    Department of Immunology Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14366Homo sapiensMutation(s): 0 
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 3NW

Download Ideal Coordinates CCD File 
B [auth A]1-[2-(2-{[2-(dimethylamino)ethyl]amino}-6-{2-[(1-methylethyl)amino]-1,3-thiazol-5-yl}pyrimidin-4-yl)benzyl]-3-ethylurea
C24 H34 N8 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
3NW PDBBind:  3NWW IC50: 7 (nM) from 1 assay(s)
BindingDB:  3NWW IC50: 7 (nM) from 1 assay(s)
Binding MOAD:  3NWW IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.09 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.155α = 90
b = 75.055β = 90
c = 78.628γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2010-09-08 
  • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2020-09-02
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references