A computational protocol was applied to identify molecular scaffolds untested toward the c-Src tyrosine kinase. A combination of docking and dynamics calculations allowed us to build three-dimensional models of the complexes between Src and several of its known inhibitors. Interactions most contributing to activity of the inhibitors, in terms of hydrogen bonds and hydrophobic contacts, were codified into pharmacophoric models that were in turn applied to perform a search of commercially available compounds within the Asinex database. As a result, we identified 1,3,4-thiadiazoles and pyrazolydine-3,5-diones showing inhibitory activity in the submicromolar range in a cell-free assay toward Src. Moreover, since several of the compounds used to generate pharmacophores were also known as Abl inhibitors, we tested the identified hits toward Abl tyrosine kinase, finding activity in the submicromolar range. Such biological data suggested that the computational protocol is an efficient tool for identifying new hits toward both Src and Abl.