Vaccinia virus, the prototype of the Poxviridae family, acquires its membrane from cytoplasmic membrane precursors assembled onto a viral protein scaffold formed by the D13 protein. This morphogenesis step is specific to the virus, utilising a set of viral membrane assembly proteins that do not have cellular counterparts but are conserved across poxviruses. We have shown that rifampicin inhibits this assembly step by competition with A17, the viral membrane protein tethering the D13 scaffold to the growing membrane (1). The low potency of rifampicin and the rapid emergence of resistant mutant viruses limit the use of the antibiotic as an antiviral drug (2). We used a fragment-based drug discovery approach to identify fragments that block the D13-A17 interaction. The primary screen used saturation transfer difference (STD) and CPMG NMR. From a library of 1137 compounds, we identified 25 hit compounds that binds to D13, among which 2 competed with A17. The crystal structures of 4 analogues of these 2 compounds in complex with D13 reveal that they all bind in the central channel of the D13 trimer, close to the F-ring previously proposed to be the A17 binding site. Together the data suggest that D13 is amenable to the development of assembly inhibitors to help understand viral morphogenesis and ultimately provide new therapeutic options against poxviral diseases in animals and humans.