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. 2021 Jun 29;6(27):17609–17620. doi: 10.1021/acsomega.1c02159

Figure 2.

Figure 2

Representative conformation of apo-TNKS2 during the last 550 ns (250–800 ns) of MD trajectory. (Left) The ligand binding pocket is depicted using a ribbon model. Several key residues (Gly1032, Phe1035, His1048, Tyr1050, Tyr1060, Ser1068, and Tyr1071) are shown using a green stick model. The α3 helix, D-loop, and G-loop regions are shown in magenta. The cyan dotted lines indicate the distance between the geometric center of the Tyr1050 phenyl ring and that of the Tyr1070 (the ring distance of Tyr1050–Tyr1071) (Å) and the minimum distance between the Phe1035 and His1048 side chains (heavy atoms; the minimum distance of Phe1035–His1048) (Å). This conformation shows that the NI-closed/AD-closed formed because the AD subsite remained in the closed conformation and the NI subsites became narrow compared to those observed in the experimental structure of apo-TNKS2 (Figure 1 and Table S1). (Right) The ligand binding pocket is depicted using a molecular surface representation. The hydrophilic and lipophilic regions are drawn in purple and green, respectively. These figures are the same view of the structures depicted in Figure 1.