4PV0

Crystal structure of spleen tyrosine kinase (Syk) in complex with an imidazopyrazine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of GS-9973, a Selective and Orally Efficacious Inhibitor of Spleen Tyrosine Kinase.

Currie, K.S.Kropf, J.E.Lee, T.Blomgren, P.Xu, J.Zhao, Z.Gallion, S.Whitney, J.A.Maclin, D.Lansdon, E.B.Maciejewski, P.Rossi, A.M.Rong, H.Macaluso, J.Barbosa, J.Di Paolo, J.A.Mitchell, S.A.

(2014) J Med Chem 57: 3856-3873

  • DOI: https://doi.org/10.1021/jm500228a
  • Primary Citation of Related Structures:  
    4PUZ, 4PV0

  • PubMed Abstract: 

    Spleen tyrosine kinase (Syk) is an attractive drug target in autoimmune, inflammatory, and oncology disease indications. The most advanced Syk inhibitor, R406, 1 (or its prodrug form fostamatinib, 2), has shown efficacy in multiple therapeutic indications, but its clinical progress has been hampered by dose-limiting adverse effects that have been attributed, at least in part, to the off-target activities of 1. It is expected that a more selective Syk inhibitor would provide a greater therapeutic window. Herein we report the discovery and optimization of a novel series of imidazo[1,2-a]pyrazine Syk inhibitors. This work culminated in the identification of GS-9973, 68, a highly selective and orally efficacious Syk inhibitor which is currently undergoing clinical evaluation for autoimmune and oncology indications.


  • Organizational Affiliation

    Department of Chemistry, ‡Department of Biology, and §Department of Drug Metabolism, Gilead Sciences, Inc. , Branford, Connecticut 06405, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK275Homo 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
Binding Affinity Annotations 
IDSourceBinding Affinity
CG4 Binding MOAD:  4PV0 Kd: 4 (nM) from 1 assay(s)
BindingDB:  4PV0 Kd: 4 (nM) from 1 assay(s)
IC50: 0.84 (nM) from 1 assay(s)
EC50: 175 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.788α = 90
b = 84.972β = 90
c = 90.308γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description