Docking of RPR into hERG1 Structure

Docking of RPR into the recently solved cryo-EM structure of hERG1 (open state, PDB: 5VA1, Wang and Mackinnon, 2017 (link)) was performed using the program Gold 4.0.1 (Cambridge DataCentre, Cambridge, United Kingdom) (Jones et al., 1995 (link)). To introduce protein flexibility, 20 snapshots, derived from previous WT hERG1 all-atom molecular dynamics simulations were used for docking (Zangerl-Plessl et al., 2020 (link)). Coordinates of the geometric center calculated among residues V549, L550, L553, F557, N658, I662, L666 and R681 (Perry et al., 2007 (link); Gardner and Sanguinetti, 2015 (link)) were taken as binding site origin. The side chains of these residues were kept flexible. The binding site radius was set to 15 Å and 150,000 operations of the GOLD genetic algorithm were used to dock the compound.