4PUZ

Crystal structure of spleen tyrosine kinase (Syk) in complex with GS-9973


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

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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 SYK
A, B
291Homo 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
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
CG9
Query on CG9

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-(1H-indazol-6-yl)-N-[4-(morpholin-4-yl)phenyl]imidazo[1,2-a]pyrazin-8-amine
C23 H21 N7 O
XSMSNFMDVXXHGJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CG9 BindingDB:  4PUZ IC50: min: 7.7, max: 1.94e+4 (nM) from 7 assay(s)
EC50: min: 2, max: 1900 (nM) from 7 assay(s)
Binding MOAD:  4PUZ IC50: 7.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.882α = 98.67
b = 41.877β = 90.43
c = 87.405γ = 101.38
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description