Fig. 12
From: Affinity of drug candidates binding to SARS-CoV-2 PLpro assessed using a generalized-ensemble method
Complex structure picked from each cluster obtained from clustering parameter Set 1 of \(\:{\upalpha\:}=\) PLpro–XR8-23 system (Table 3). Panels (a–c) are respectively 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 \(\:{Cls}_{3}^{\left({\upalpha\:}\right)}\left(\text{S}\text{e}\text{t}\:1\right)\).The orange segment is the loop region (\(\:{G}_{A}^{\left(RC1\right)}\); residues 266–271). The green one is a part of helix (\(\:{G}_{B}^{\left(RC1\right)}\) ; residues 165–168): Fig. 1b shows details for these segments. Side-chains of two amino-acid residues Y268 and Q269 are labeled. Cornflower blue molecules are compounds, with broken-line circles representing their core regions (Fig. S5 of SI).
