Figure 9 | Scientific Reports

Figure 9

From: Comprehensive in vitro characterization of PD-L1 small molecule inhibitors

Figure 9

Evaluating the binding of Aurigene-1 against hPD-L1 using computational approaches. (A) The root mean square deviation matrix of all the 48 PD-L1 structures in PDB shows that there are no significant conformational differences in PD-L1 while binding to different partners (PD-1, small molecules, monoclonal antibodies and large peptides). (B) Identification of different binding pockets (shown as yellow dummy atoms) on the surfaces of all the PD-L1 structures (shown as VdW representations in blue) using Site Finder module in MOE program. Here, the PD-1 protein is shown as a line-surface illustration with ~60% transparency, in order to show the PD-1 binding face on PD-L1. (C) The 3D structures showing different docking poses of Aurigene-1 within different binding pockets in PD-L1 (shown as blue surface). (D) Comparison of the calculated Delta G binding for all the binding poses of Aurigene-PD-L1 complexes and the top-most pose of BMS-small molecules-PD-L1 complexes (shown with a circle).

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