Fig. 7. Molecular docking and molecular dynamic simulation analyses of the YM201636’s bindings in human TPC2.

a, b The top 30 poses of YM201636 docked in the whole channel pore region (a) or the pore entrance region (b) of the PI(3,5)P₂-bound open-state channels. The YM201636’s carbon atom in (a) is shown in green and yellow, respectively, for the poses with their 6-amino-nicotinamide group pointed in and out of the pore. c The bottom views of the four representative poses (upper panels) and the side-views of the superimposed YM201636’s conformations (50 frames; 2 ns/frame) during the 100 ns simulation (bottom). For clarity, only a representative protein structure from a single frame is shown in (a–c). d Plots of the mean contact scores and total contact times for residues interacting with YM201636. The data were obtained by analyses of their interactions in the trajectories of the four 100 ns molecular dynamic simulations with the Pycontact program. The scores and time were combined from the two identical residues of the two homodimeric subunits.