The binding pocket of RUC-1 studied by molecular dynamics (MD) simulations. (A) Comparison of the binding site of RUC-1 in crystal structure (magenta) and in a representative conformation (at 8 nanoseconds) of the last 5 nanoseconds of a 10-nanosecond MD simulation (cyan). The structures were aligned on the α_IIb β-propeller domain by Pymol. α_IIb and β₃ subunits are shown in light blue and wheat, respectively. (B-D) Specific distance changes during 10-nanosecond MD simulations. Values for crystal structure are indicated by triangles. (B) Minimum distance between the basic nitrogen of RUC-1 and either of the 2 oxygens of the Asp-224 side chain (blue line). Minimum distance between either of the 2 oxygens of the Asp-224 side chain and the backbone nitrogen of Trp-162 (red line). (C) Distance between the oxygen of the Tyr-190 side chain and the backbone carbonyl oxygen of β₃ Arg-216 (blue line). Distance between the centroid of the aromatic ring of Tyr-190 side chain and the centroid of the RUC-1 fused ring (orange line). (D) Number of water molecules either forming direct interactions with the RUC-1 carbonyl oxygen or interacting with the carboxyl oxygens of the Asp-232 side chain.