The ubiquitin-proteasome system (UPS) relies on exquisitely regulated protein interactions to achieve the specific and dynamic regulation of its many substrates. The SCF ubiquitin ligases employ a cohort of receptors called F-box proteins that recognize substrates through dedicated protein interaction domains, often in a phosphorylation-dependent manner. A number of F-box proteins play a critical role in cancer, most notably Skp2, Fbw7/hCdc4 and b-TrCP, which collectively mediate the elimination of a host of tumour suppressor proteins and/or oncoproteins. Allosteric control appears to be a prevalent regulatory theme in the UPS and is often constructed from low affinity interactions in multi-subunit complexes. In an unexpected example of allostery, we identified a small molecule inhibitor of Cdc4 called SCF-I2 that blocks substrate recognition. SCF-I2 binds at a site far removed from the phosphopeptide binding pocket on the WD40 domain of Cdc4 but elicits a series of structural alterations that result in occlusion of the binding pocket. In another example, we characterized a small molecule called CC0651 that inactivates the E2 enzyme Cdc34 by a non-catalytic site mechanism. Cdc34 catalyzes the ubiquitination of hundreds of proteins in conjunction with the cullin-RING (CRL) superfamily of E3 enzymes, of which the SCF enzymes are the archetype. CC0651 analogs inhibit proliferation of human cancer cell lines and cause accumulation of the SCFSkp2 substrate p27Kip1. Structure determination revealed that CC0651 inserts into a cryptic binding pocket on Cdc34 distant from the catalytic site to cause subtle but wholesale changes in E2 structure. The changes induced by CC0651 appear to interfere with the discharge of ubiquitin to acceptor lysine residues. Notably, because Cdc34 is the dedicated E2 for the CRL superfamily, inhibition of Cdc34 may phenocopy the anti-cancer effects of the Nedd8 activating enzyme inhibitor MLN4924, which attenuates all CRL activity and currently shows promise in early stage clinical trials. More generally, the entire family of 38 E2 enzymes in humans are in principle susceptible to non-catalytic site inhibition, and hence represent a viable new class of drug target in the cancer.