Fig. 6
From: Affinity of drug candidates binding to SARS-CoV-2 PLpro assessed using a generalized-ensemble method
Contact map between PLpro (X-axis) and GRL0617 (Y axis) for each cluster with clustering parameter Set 1 (Table 3). The contact probability, which is normalized in each cluster, is presented by color scale. Panels (a–c) are for clusters \(\:{Cls}_{1}^{\left({\upalpha\:}\right)}\left(\text{S}\text{e}\text{t}\:1\right)\), \(\:{Cls}_{2}^{\left({\upalpha\:}\right)}\left(\text{S}\text{e}\text{t}\:1\right)\) and \(\:{Cls}_{3}^{\left({\upalpha\:}\right)}\left(\text{S}\text{e}\text{t}\:1\right)\) of \(\:{\upalpha\:}=\) PLpro–GRL0617 system. Only the names of atoms in the core region are displayed on the Y axis (Fig. S5 of SI). Small green rings denote the position of atom group \(\:{G}_{A}^{\left(RC1\right)}\) (residues 266–271) and \(\:{G}_{B}^{\left(RC1\right)}\) (residues 165–168) (Fig. 1b). Space between \(\:{G}_{A}^{\left(RC1\right)}\) and \(\:{G}_{B}^{\left(RC1\right)}\) corresponds to the ligand-binding site. The green rectangle represents C111 of PLpro contacting the core-region of the compounds.
