3EMG

Discovery and SAR of novel 4-thiazolyl-2-phenylaminopyrimidines as potent inhibitors of spleen tyrosine kinase (SYK)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and SAR of novel 4-thiazolyl-2-phenylaminopyrimidines as potent inhibitors of spleen tyrosine kinase (SYK).

Farmer, L.J.Bemis, G.Britt, S.D.Cochran, J.Connors, M.Harrington, E.M.Hoock, T.Markland, W.Nanthakumar, S.Taslimi, P.Ter Haar, E.Wang, J.Zhaveri, D.Salituro, F.G.

(2008) Bioorg Med Chem Lett 18: 6231-6235

  • DOI: https://doi.org/10.1016/j.bmcl.2008.09.106
  • Primary Citation of Related Structures:  
    3EMG

  • PubMed Abstract: 

    A series of SYK inhibitors based on the phenylamino pyrimidine thiazole lead 4 were prepared and evaluated for biological activity. Lead optimization provided compounds with nanomolar K(i)'s against SYK and potent inhibition in mast cell degranulation assays.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Vertex Pharmaceuticals, Inc., 130 Waverly Street, Cambridge, MA 02139, USA. luc_farmer@vrtx.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK291Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
GTEx:  ENSG00000165025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43405
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
685
Query on 685

Download Ideal Coordinates CCD File 
B [auth A]2-{2-[(3,5-dimethylphenyl)amino]pyrimidin-4-yl}-N-[(1S)-2-hydroxy-1-methylethyl]-4-methyl-1,3-thiazole-5-carboxamide
C20 H23 N5 O2 S
PEGXADGTBNRSGV-ZDUSSCGKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
685 BindingDB:  3EMG Ki: 9 (nM) from 1 assay(s)
IC50: min: 6, max: 70 (nM) from 2 assay(s)
PDBBind:  3EMG Ki: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.87α = 90
b = 84.45β = 99.63
c = 41.44γ = 90
Software Package:
Software NamePurpose
SCALAdata processing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2008-12-02 
  • Deposition Author(s): Ter Haar, E.

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations