Table 4.
Intermolecular interactions appearing in the structural complexes of the identified compounds with SARS-CoV-2 MPro.
| Ligand | Hydrogen bond1 | Van der Waals contacts2 | Salt bridges and π-π interactions3 |
|---|---|---|---|
| I | O1…**HN[S144] O2…**HN[H163] O3…*HN[E166] | H41(3), M49(1), L141(3), N142(1), M165(6), E166(3), D187(2), Q189(1) | COO…H163 H41 (Т-stacking) |
| II | O1H…*O[M49] | T25(1), H41(2), M165(3), L167(1), P168(1), Q189(1), Q192(1) | − |
| III | O1H…*N[L141] O2H…*N[G143] O2…*NH[G143] O1…**HN[H163] | H41(4), C44(1), M49(1), M165(4), L141(2), N142(1), E166(2), Q189(5) | NCHC…E166 H41 (Т- и π-stacking) |
| IV | O1H…*O[C44] N1…*HN[E166] O2…*HN[T190] O2…**HN[Q192] | T25(2), H41(1), C44(1), M49(1), M165(3), Q189(4) | H41 (Т-stacking) |
| V | O1…*HN[E166] | C44(2), M49(1), L141(1), N142(1), M165(4), E166(1), R188(1) | − |
Footnotes: 1Atoms of the ligands are shown first, followed by the corresponding atoms of SARS-CoV-2 MPro (MPro residues are in brackets in one-letter code). Symbol * denotes the atoms of the residue main chain, and symbol ** marks the atoms of the residue side chain. 2Amino acids of SARS-CoV-2 MPro forming van der Waals contacts with the ligands. The number of contacts is given in brackets. 3For salt bridges, the functional groups of ligands are shown first, followed by the residues of SARS-CoV-2 MPro. For π- or T-stacking, residue of SARS-CoV-2 MPro involved in these interactions is shown.