Figure 3.

(A, B) Predicted bound conformations of QND. KCNT1 subunits are depicted in gray, gold, white, and blue cartoons and sticks, while QND is represented in yellow sticks. Direct H-bonds are represented as magenta dashed lines, water-mediated H-bonds as orange dashed lines, π–π stacking interactions as green dashed lines, and π-cation interactions as red dashed lines. In (A, B), for reference, F312 and F346 are always shown as sticks and the experimental bound conformation of C23 is shown in white transparent sticks. (C) RMSD of QND as a function of MD simulation time. (D) Quindine/KCNT1 interaction diagram. Only residues interacting with the ligand for at least 144 out of 960 ns of MD simulation are shown. Residues are colored according to the following scheme: cyan, polar; green, hydrophobic; gray, water molecule. Gray halos highlight solvent exposure. H-bonds are represented by magenta arrows (dashed when side-chain atoms are involved, solid in the case of backbone atoms involvement); green solid lines represent π–π stacking interactions; red solid lines represent π-cation interactions.