Crystal structure of an inhibitor-bound Syk

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Crystal structures of spleen tyrosine kinase in complex with novel inhibitors: structural insights for design of anticancer drugs

Lee, S.J.Choi, J.S.Han, B.G.Kim, H.S.Song, H.J.Lee, J.Nam, S.Goh, S.H.Kim, J.H.Koh, J.S.Lee, B.I.

(2016) FEBS J 283: 3613-3625

  • DOI: https://doi.org/10.1111/febs.13831
  • Primary Citation of Related Structures:  
    4XG2, 4XG3, 4XG4, 4XG6, 4XG7, 4XG8, 4XG9, 5GHV

  • PubMed Abstract: 

    Spleen tyrosine kinase (SYK) is a cytosolic nonreceptor protein tyrosine kinase that mediates key signal transduction pathways following the activation of immune cell receptors. SYK regulates cellular events induced by the B-cell receptor and Fc receptors with high intrinsic activity. Furthermore, SYK has been regarded as an attractive target for the treatment of autoimmune diseases and cancers. Here, we report the crystal structures of SYK in complex with seven newly developed inhibitors (G206, G207, O178, O194, O259, O272, and O282) to provide structural insights into which substituents of the inhibitors and binding regions of SYK are essential for lead compound optimization. Our kinase inhibitors exhibited high inhibitory activities against SYK, with half-maximal inhibitory concentrations (IC 50 ) of approximately 0.7-33 nm, but they showed dissimilar inhibitory activities against KDR, RET, JAK2, JAK3, and FLT3. Among the seven SYK inhibitors, O272 and O282 exhibited highly specific inhibitions against SYK, whereas O194 exhibited strong inhibition of both SYK and FLT3. Three inhibitors (G206, G207, and O178) more efficiently inhibited FLT3 while still substantially inhibiting SYK activity. The binding mode analysis suggested that a highly selective SYK inhibitor can be developed by optimizing the functional groups that facilitate direct interactions with Asn499.

  • Organizational Affiliation

    Genosco, Cambridge, MA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK290Homo sapiensMutation(s): 0 
Gene Names: SYK
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on X4G

Download Ideal Coordinates CCD File 
B [auth A](3R)-1-{[1-(5-fluoro-2-{[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]amino}pyrimidin-4-yl)-4-methyl-1H-pyrrol-3-yl]methyl}pyrrolidin-3-ol
C24 H30 F N5 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
X4G Binding MOAD:  4XG4 IC50: 21.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.219α = 90
b = 85.056β = 98.8
c = 41.749γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2016-10-19
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description