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 1.1 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYKA275Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CG4 (Subject of Investigation/LOI)
Query on CG4

Download Ideal Coordinates CCD File 
B [auth A]4-[(3-{8-[(3,4-dimethoxyphenyl)amino]imidazo[1,2-a]pyrazin-6-yl}benzoyl)amino]benzoic acid
C28 H23 N5 O5
VCLOZUGEZMWXFF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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