The 'mutate & conjugate' methodology allows for the rapid development of selective probes to investigate the biological function of target proteins or protein domains, circumventing the limitations normally encountered while developing chemical probes. Although we selected BRD4 as the ideal target to test our methodology, this approach can be potentially applied to newly emerging or poorly understood targets, for which no selective ligands are yet available. In this work we compared two different approaches; a structure-based method and screening of a diverse set of fragments, and in this case the latter proved more effective. With the advancement of CRISPR-Cas9 technologies and site-directed mutagenesis of endogenous proteins the application of 'mutate & conjugate' will improve the reliability of target validation and phenotypic studies while expanding the ligandable proteome.