Table 2.
The most important interactions of the GRL0617 (PDB code: 7CMD) and compound 107 (PDB code: 7LBR) in the active site of SARS-CoV-2 PLpro were analyzed by Discovery Studio Visualizer v4.5.
| Interaction | Compound 107 |
GRL0617 |
||||
|---|---|---|---|---|---|---|
| Residues | Interacting groups | Distance (Å) | Residues | Interacting groups | Distance (Å) | |
| Conventional H-bond | Gln269 | Carbonyl group | 1.87 | Gly269 | Carbonyl group | 2.37 |
| Asp164 | NH (Amide) | 1.71 | Asp164 | NH (Amide) | 2.79 | |
| – | – | – | Tyr264 | Carbonyl group | 2.66 | |
| Pi-Alkyl | Tyr264 | CH3 (A-Phenyl ring) | 4.84 | Tyr264 | CH3 (A-Phenyl ring) | 4.60 |
| Pro248 | B-Phenyl ring | 4.45 | Pro248 | Naphthyl moiety | 4.51 | |
| Pro248 | Th-ring | 4.97 | Pro248 | Naphthyl moiety | 4.13 | |
| – | – | – | Tyr273 | CH3 (A-Phenyl ring) | 5.45 | |
| Amide-Pi Stacked | Asn267 | Th-ring | 5.12 | – | – | – |
| Pi-Sigma | Asp164 | A-Phenyl ring | 2.59 | Asp164 | A-Phenyl ring | 2.72 |
| – | – | – | Gln269 | A-Phenyl ring | 2.86 | |
| – | – | – | Tyr268 | Naphthyl moiety | 3.01 | |
| Pi-Pi T-Shaped | Tyr268 | A-Phenyl ring | 5.25 | Tyr268 | A-Phenyl ring | 5.08 |
| Tyr268 | B-Phenyl ring | 4.75 | Tyr268 | Naphthyl moiety | 5.02 | |
| – | – | – | Tyr268 | Naphthyl moiety | 5.24 | |
| Carbon | Tyr268 | Carbonyl group | 2.56 | Tyr268 | Carbonyl group | 2.64 |
| Gln269 | Azetidine | 3.00 | – | – | – | |
| Gly266 | CH2 (Adj to Th-ring) | 2.74 | – | – | – | |
| Alkyl | Leu162 | CH3 (A-Phenyl ring) | 4.10 | Leu162 | CH3 (A-Phenyl ring) | 4.36 |
| Pi-Sulfur | Tyr264 | S (Th-ring) | 5.52 | – | – | – |