N-myristoyltransferase inhibitors (NMTi) are promising novel anti-cancer agents, including in MYCN-amplified neuroblastoma and Burkitt’s lymphoma, but a mechanistic rationale for targeted therapy is still poorly defined. A key function of N-myristoylation is to mediate membrane localisation. We therefore carried out membrane proteomics on the P493-6 cell line +/- NMTi. Identification of PPIs between affected proteins via STRING allowed the identification of heavily affected biological nodes, including respiratory complex I. This study provides a mechanistic rationale for NMTi in MYC-deregulated cancers.