The development of small-molecule inhibitors of Hemagglutinin of the influenza virus could be relevant to oppose the diffusion of new pandemic viruses. In this work, we made use of NMR spectroscopy to study the interaction between two derivatives of sialic acid, Neu5Ac-α-(2,6)-Gal-β-(1-4)-GlcNAc and Neu5Ac-α-(2,3)-Gal-β-(1-4)-GlcNAc, and hemagglutinin directly expressed on the surface of recombinant human cells. We analyzed the interaction of these trisaccharides with 293T cells transfected with the H5- and H1 variants of hemagglutinin, which thus retains its native trimeric conformation in such a realistic environment. Exploiting the magnetization transfer between the protein and the ligand, we obtained evidence of the binding event and identified the epitope. We analyzed the conformational features of the glycans with an approach that combines NMR spectroscopy and data-driven molecular dynamics simulations, thus obtaining useful information for an efficient drug design.