Fig. 3: Ι In silico docking of CQ to simulated conformations of PfCRTDd2. | Nature Communications

Fig. 3: Ι In silico docking of CQ to simulated conformations of PfCRTDd2.

From: pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle

Fig. 3

a Location of E207 (represented as sticks, with carbons in yellow) between transmembrane helices 5 and 6 (TM5 and TM6) in the open-to-vacuole conformation of PfCRTDd2. Note that the carboxyl side chain points into the cavity space. b Predicted binding modes of CQ (in orange) for different conformations of PfCRT (open-to-vacuole, occluded, open-to-cytoplasm) and different protonation states of E207 (in purple). Protein configurations were obtained from three independent 200-ns MD simulations, and clustered. CQ was docked to the centers of the clusters. Only the pose obtained for the most populated cluster is shown. Docking was performed using AutoDock Vina. Residues within a distance of 4 Å from CQ are shown in green. Source data are provided as a Source Data file87.

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