3NWW

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.3 of the entry. See complete history. 


Literature

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: 10.1016/j.bmcl.2010.07.102
  • Primary Citation of Related Structures:  
    3NWW

  • 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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A366Homo sapiensMutation(s): 0 
Gene Names: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2, SAPK2A
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3NW
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
JQWPDTBHOVYRPB-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3NW Binding MOAD:  3NWW IC50: 7 (nM) from 1 assay(s)
BindingDB:  3NWW IC50: 7 (nM) from 1 assay(s)
PDBBind:  3NWW IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2010-07-12 
  • 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