Significance Drugs that inhibit specific kinases now represent one of the main classes of targeted therapies. A majority of drug development efforts in this space focus on a given kinase in isolation as the target. However, our work demonstrates that in the context of the RAF/MEK/ERK pathway, the relevant target for compounds developed as allosteric MEK inhibitors (MEKi) is not free MEK but RAF/MEK complexes. Because signaling through this pathway is essential in normal tissues, indiscriminate blockade of all MEK activity is not tolerated. Our findings imply that selective inhibition of specific RAF/MEK complexes is an accessible route for development of new MEKi, and they provide a biophysical foundation for better understanding and applying current clinical agents.