Fig. 3.

Binding of tanshinone IIA sulfonate sodium in the PLpro active pocket. a) The representative conformation of the stable binding mode found by docking and MD simulations. The pocket region is rotated and zoomed on the right panel for a clearer view. PLpro is shown in green, pocket residues in blue, tanshinone IIA sulfonate sodium in yellow and the PLpro residues within 3 Å of tanshinone IIA sulfonate sodium in cyan. b) The heavy-atom RMSD of tanshinone IIA sulfonate sodium with the representative conformation as the reference. c) The distance between the center of mass (COM) of tanshinone IIA sulfonate sodium and the COM of Tyr268 side chain, and between the COM of tanshinone IIA sulfonate sodium and the CZ (the terminal carbon) atom of Arg166 side chain. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)