DGY-06-116, a novel and selective covalent inhibitor of SRC kinase

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

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Structure and Characterization of a Covalent Inhibitor of Src Kinase.

Gurbani, D.Du, G.Henning, N.J.Rao, S.Bera, A.K.Zhang, T.Gray, N.S.Westover, K.D.

(2020) Front Mol Biosci 7: 81-81

  • DOI: https://doi.org/10.3389/fmolb.2020.00081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Unregulated Src activity promotes malignant processes in cancer, but no Src-directed targeted therapies are used clinically, possibly because early Src inhibitors produce off-target effects leading to toxicity. Improved selective Src inhibitors may enable Src-directed therapies. Previously, we reported an irreversible Src inhibitor, DGY-06-116, based on the hybridization of dasatinib and a promiscuous covalent kinase probe SM1-71. Here, we report biochemical and biophysical characterization of this compound. An x-ray co-crystal structure of DGY-06-116: Src shows a covalent interaction with the kinase p-loop and occupancy of the back hydrophobic kinase pocket, explaining its high potency, and selectivity. However, a reversible analog also shows similar potency. Kinetic analysis shows a slow inactivation rate compared to other clinically approved covalent kinase inhibitors, consistent with a need for p-loop movement prior to covalent bond formation. Overall, these results suggest that a strong reversible interaction is required to allow sufficient time for the covalent reaction to occur. Further optimization of the covalent linker may improve the kinetics of covalent bond formation.

  • Organizational Affiliation

    Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 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, C, D, E
A, B, C, D, E, F, G, H
276Homo sapiensMutation(s): 0 
Gene Names: SRCSRC1
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens)
Explore P12931 
Go to UniProtKB:  P12931
PHAROS:  P12931
GTEx:  ENSG00000197122 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12931
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.534α = 89.962
b = 84.028β = 90.046
c = 120.109γ = 90.118
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 2.0: 2019-12-11
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2020-06-24
    Changes: Database references
  • Version 2.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description