6E6E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

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: 10.3389/fmolb.2020.00081
  • Primary Citation of Related Structures:  
    6E6E

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src ABCDEFGH276Homo sapiensMutation(s): 0 
Gene Names: SRCSRC1
EC: 2.7.10.2
Find proteins for P12931 (Homo sapiens)
Explore P12931 
Go to UniProtKB:  P12931
NIH Common Fund Data Resources
PHAROS:  P12931
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HVY
Query on HVY

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H
N-(2-chloro-6-methylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-4-{[2-(propanoylamino)phenyl]amino}pyrimidine-5-carboxamide
C32 H35 Cl N8 O2
BHJOOAYUNMSUFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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