Different modes of action small molecule inhibitors provide versatile tools for investigation of biology and development of therapeutics. However, to evaluate their exact mechanism of actions remains to be a challenging tas. We have identified two classes of p97 inhibitors, ATP competitive and allosteric inhibitors. We initially showed that the allosteric phenyl indole p97 inhibitor, UPCDC-30245, does not affect on two well-known cellular functions of p97, Endoplasmic-reticulum-associated protein degradation (EARD) and unfolded protein response (UPR) pathway dramatically, instead strongly increases the lapidated form of microtubule-associated proteins 1A/1B light chain 3B (LC3-II). To evaluate the molecular mechanism of UPCDC-30245, we performed proteomic analysis of UPCDC-30245 treated cells. Our results revealed UPCDC-30245 blocks endo-lysosomal degradation via inhibiting the formation of early endosome and reducing the acidity of lysosome and this is aa potential off-target effect. More importantly, we demonstrated UPCDC-30245 exhibits promising ntiviral effects via blocking virus entry and this could be due to both on-target and off-target effect.