Nannocystin A is a potent antiproliferative cyclodepsipeptide targeting eukaryotic translation elongation factor 1α. To elucidate the binding role of its (2R,3S)-epoxide, we designed and synthesized a focused library of 10 nannocystin analogues. Variable temperature NMR experiments demonstrated the importance of the (2R,3S)-epoxide in controlling the macrocyclic conformation. Biological evaluation of these compounds against three typical cancer cell lines established a clear structure-activity relationship at the epoxide region, which was rationalized by comparing the superimposed conformations of different nannocystin analogues and in silico docking analysis. Our results showed that the (2R,3S)-epoxide of nannocystin A is mainly responsible for controlling the macrocyclic conformation, rather than binding directly to the target.