Crystal structure of c-SRC in complex with a covalent lysine probe

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes.

Zhao, Q.Ouyang, X.Wan, X.Gajiwala, K.S.Kath, J.C.Jones, L.H.Burlingame, A.L.Taunton, J.

(2017) J Am Chem Soc 139: 680-685

  • DOI: https://doi.org/10.1021/jacs.6b08536
  • Primary Citation of Related Structures:  
    5K9I, 5U8L

  • PubMed Abstract: 

    Protein kinases comprise a large family of structurally related enzymes. A major goal in kinase-inhibitor development is to selectively engage the desired kinase while avoiding myriad off-target kinases. However, quantifying inhibitor interactions with multiple endogenous kinases in live cells remains an unmet challenge. Here, we report the design of sulfonyl fluoride probes that covalently label a broad swath of the intracellular kinome with high efficiency. Protein crystallography and mass spectrometry confirmed a chemoselective reaction between the sulfonyl fluoride and a conserved lysine in the ATP binding site. Optimized probe 2 (XO44) covalently modified up to 133 endogenous kinases, efficiently competing with high intracellular concentrations of ATP. We employed probe 2 and label-free mass spectrometry to quantify intracellular kinase engagement by the approved drug, dasatinib. The data revealed saturable dasatinib binding to a small subset of kinase targets at clinically relevant concentrations, highlighting the utility of lysine-targeted sulfonyl fluoride probes in demanding chemoproteomic applications.

  • Organizational Affiliation

    Worldwide Research and Development, Pfizer , San Diego, California 92121, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusMutation(s): 0 
Gene Names: SRC
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00523
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on O44

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-[(4-{4-[(3-cyclopropyl-1H-pyrazol-5-yl)amino]-6-[(prop-2-yn-1-yl)carbamoyl]pyrimidin-2-yl}piperazin-1-yl)methyl]benzene-1-sulfonyl fluoride
C25 H27 F N8 O3 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.012α = 78.85
b = 63.306β = 88.75
c = 73.77γ = 89.93
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
CSCChinaNO. 201409110014

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release