Figure 6: Representation of C5aR-3D53 interactions at multiple time points in MD simulations. | Scientific Reports

Figure 6: Representation of C5aR-3D53 interactions at multiple time points in MD simulations.

From: Receptor residence time trumps drug-likeness and oral bioavailability in determining efficacy of complement C5a antagonists

Figure 6

C5aR-3D53 complex at (A) 10 ns: Arg6 of 3D53 faced towards ECL2 and made a short-lived contact with the Cys188 backbone carbonyl oxygen. (B) 50 ns: Arg6 underwent a large shift involving re-location and formation of an electrostatic interaction with Asp282, accompanied by movement of the top region of TM2 to shorten the distance to TM7. (C) 80 ns: similar protein-ligand interactions as at 50 ns, reflecting stable and long-lasting interactions between 3D53 and C5aR. Hydrogen bonds are depicted as dotted lines. (D) Distance measurements between stated residues and TM helices throughout MD simulations. (E) Root mean square fluctuation (RMSF) of C5aR residue sidechains throughout MD simulations.

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