Figure 4.
Fig. 4. Molecular recognition interactions in the
substrate-analogue hexapetidyl CMK inhibitor
(Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK) complexed with SARS Mpro. (A)
A stereoview of the substrate-binding pocket (green) in protomer
A of the CMK inhibitor complex. The inhibitor molecule (red) is
shown in the 2.5-Å original F[o] - F[c] difference
electron-density map (1.5 ). Hydrogen bonds are
shown as dashed lines. The Gln-P1 is bound to the S1
substrate-specificity subsite, but Leu-P2 fails to bind at the
S2 subsite (near Asp-A187), which is instead occupied by Thr-P3.
The amino acid residues of the protein are labeled in single
letters; for example, H163A stands for His-163 of monomer A
(i.e., His-A163). (B) A stereoview of the substrate-binding
pocket (green) in protomer B of the CMK inhibitor complex. The
inhibitor molecule (red) is shown in the original F[o] - F[c]
difference electron-density map (1.5 ). The Gln-P1 does not
bind to the partly collapsed S1 subsite in this protomer, but
Leu-P2 and Ser-P4 are in their canonical binding sites. See text
for further details.
). Hydrogen bonds are
shown as dashed lines. The Gln-P1 is bound to the S1
substrate-specificity subsite, but Leu-P2 fails to bind at the
S2 subsite (near Asp-A187), which is instead occupied by Thr-P3.
The amino acid residues of the protein are labeled in single
letters; for example, H163A stands for His-163 of monomer A
(i.e., His-A163). (B) A stereoview of the substrate-binding
pocket (green) in protomer B of the CMK inhibitor complex. The
inhibitor molecule (red) is shown in the original F[o] - F[c]
difference electron-density map (1.5