Fig. 3: SEE-CITE mapping of ABL1 binding sites.
From: Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics
a, Structures of dasatinib and asciminib probes. b, Competitive gel-based AfBPP analysis of recombinant ABL1 kinase domain (1 μM) in HEK293T lysates (0.5 mg ml−1) pretreated with dasatinib or asciminib (0.5 h) followed by 4c or 5c probe treatment (1 μM, 0.5 h). Representative data are presented for n = 3 independent experiments. c, Workflow for quantitative SEE-CITE comparing 4c and 5c labelling of ABL1 kinase domain (1 μM) in lysates treated with 4c or 5c (1 μM, 0.5 h). d, Mean log2(H/L) ratios generated via IonQuant analysis with FragPipe variable search workflow and with SEE-CITE-based sites of labelling (lowercase letters) using FragPipe mass offset search workflow. *, peptide identified using MSBooster and Percolator without deisotoping in MSFragger; #, peptide identified using PeptideProphet with de-isotoping in MSFragger. e, Comparison of log2(H/L) ratios of SEE-CITE-modified ABL1 peptides (red/blue) versus unmodified peptides (grey) from n = 3 biological replicates. f, Identified labelled sites for the ABL1 kinase domain by SEE-CITE probes 4c and 5c (PDB: 2GQG for ATP pocket and 5MO4 for myristoyl pocket, respectively). All MS data can be found in Supplementary Table 5.
