N-glycosylated proteins that traverse the endoplasmic reticulum (ER) can make use of the calnexin cycle to attain their correct fold. The calnexin cycle modifies the N-glycan structure and allows for association of the glycoprotein with the ER lectins calnexin and calreticulin, which in turn recruit further chaperones that assist folding. Most enveloped viruses encode glycoproteins, which, upon infection of a host cell, crucially depend on the calnexin cycle to aid their folding. This includes diverse families such as Flaviviridae, Retroviridae and Orthomyxoviridae. We studied the calnexin cycle components with the ultimate aim of developing broad-spectrum antivirals. X-ray crystallography was used to structurally characterise the murine ER α-glucosidase I, which controls entry into the calnexin cycle, with a number of inhibitory antiviral iminosugars. These data reveal flexibility in the ligands' alkyl tails and may act as a basis for the discovery of enzyme specific inhibitors. UDP-glucose: glycoprotein glucosyltransferase (UGGT) is the quality control checkpoint of the calnexin cycle whose full-length structure from the thermophilic fungus Chaetomium thermophilum was recently determined. Presented here are a higher resolution structure in addition to SAXS studies of UGGT's interaction with Sep15, a protein that enhances UGGT activity. UGGT's reaction releases into the ER lumen UDP, which is the only known small molecule inhibitor of UGGT. An ER-resident UDPase, ENTPD5, breaks down UDP into UMP. Enzymatic characterisation of ENTPD5 reveals its substrate specificities; in addition we show a paralog, ENTPD6, possesses similar activities. Presented here is work towards crystallisation of these two proteins and a test of the anti-Zika activity of ENTPD5 inhibitors. Finally, CRISPR/Cas9 knock-out cells were generated to test, in principle, whether modulation of the activity of proteins involved in the calnexin cycle could be antiviral. The data confirm that the ER glucosidases are likely the best targets of those studied.