Fig. 6: Unbiased CG molecular dynamics simulations of inhibitor binding to ECF transporter.
From: Identification of inhibitors targeting the energy-coupling factor (ECF) transporters
a Crystal structure of ECF PanT (PDB ID 6ZG3)40, using the same color scheme and analysis as Fig. 3. Results indicated only one pocket for this ECF complex, which as P9 in ECF-FolT2 is at the interface between EcfT and the S-component. The bar plot shows calculated binding free energies (ΔGbind) of compound 1 to this pocket. The error bars represent the mean absolute error obtained by the block-averaging approach. b Compound 1: pocket P9 density in ECF-FolT2 and the pocket of ECF-PanT simulations. The solid and transparent green isosurfaces correspond to a 100- and 10-fold higher density than in the bilayer. The proximity of the low occupancy isosurface indicates the proximity of the pockets. c Representative pose of compound 1 inside the pocket of ECF-PanT. The structures were backmapped from the CG to the atomistic resolution. Some residues from EcfT (salmon) and S-component (gray) are highlighted, including the hydrogen-bond network (black, dashed lines). Hydrogen atoms have been omitted for clarity.
