AbstractThe interaction of the synthetic pentasaccharide AGA*IAM (GlcNS,6S‐GlcA‐GlcNS,3S,6S‐IdoA2S‐GlcNS,6S‐Me) with the extracellular Ig2 domain of the fibroblast growth factor receptor (FGFR2) has been studied by NMR and computational methods. Analysis of the heparin pentasaccharide in the free state and in the complex indicates the existence of a conformational selection process. Although an equilibrium exists between the 1C4 and 2S0 conformers (ratio 60:40) of the 2‐O‐sulfo‐α‐L‐iduronate ring (IdoA2S) in the free state, FGFR2 selects only the unique twisted‐boat 2S0 conformation of this IdoA2S residue. In addition, the protein residues involved in the binding with AGA*IAM have also been characterized. The NMR results obtained, from both the ligand and protein perspective, were employed to model the bound conformation of the pentasaccharide by a combined docking and molecular dynamic simulation approach.