Synthetic macrocycles (MCs) have received significant attention for their potential as drugs, largely due to their proposed utility against traditionally difficult targets. Now, Villar et al. identify and examine a representative set of MC–protein complexes for which co-crystal structures have been reported, to establish key characteristics of their binding modes. They propose guidelines for designing synthetic MC libraries with favourable structural and physicochemical features for binding to protein targets and for good bioavailability.