Fig. 3: Putative entry of BDM88832 (8) to its binding site in AcrB.
From: Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps
Figure shows the preferred cumulative location (green surfaces) of BDM88832 (8) as seen in all-atom MD simulations of several compounds placed around AcrB embedded in a phospholipid bilayer. a Side view of BDM88832 (8) density on the whole AcrB tripartite efflux pump (L, T, and O protomers are shown as blue, yellow and red, respectively). b BDM88832 (8) density distribution viewed from the cytoplasmic side with only the TM domain shown for clarity. Relevant TM helices are labelled, and dashed circles on each monomer delimit the location of the experimental binding site. c Zoomed side view of the L protomer showing accumulation of BDM88832 (8). The X-ray conformation of BDM88832 (8) in AcrB is superimposed in CPK coloured by atom type (C, N, I, and Cl in green, blue, pink, and yellow, respectively). TM helix 5 is shown transparent for clarity. All data are cumulative results from 5 independent MD simulations of 2 μs each; transparent and solid green surfaces represent iso-values of 3 and 5, respectively.
