Table 5. Binding Affinity and Interaction with the Target E. coli DNA Gyrase (PDB ID: 6F86).
| residual amino acid interactions |
||||
|---|---|---|---|---|
| compd | affinity (kcal/mol) | H-bond | hydrophobic/π-cation/π-anion/ π-alkyl interactions | van der Waals interactions |
| 1 | –4.8 | Ser121, Val97 | Ile94, Ile78 | |
| 2 | –4.4 | Ser121, Val120 | Ile94, Ile78 | |
| 3 | –4.7 | Ser121, Val120, Asp49 | Ile94, Ile78, Ala47 | |
| 4 | –5.5 | Thr165, Asn46 | Ile94, Ile78, Pro79 | |
| 5 | –6.9 | Thr165, Asn46, Arg76 | Ile94, Pro79, Glu50 | |
| 6 | –5.4 | Asn46 | Ile94, Pro79, Val71, Val43, Ala47 | |
| 7 | –5.3 | Ser121, Val120, Asn46 | Ile94, Pro79 | |
| 8 | –5.4 | Ser121, Asn46, Leu98a | Ile94, Ile78 | |
| 9 | –5.8 | Thr165, Asn46 | Ile94, Ile78, Ala47 | |
| 10 | –6.7 | Asn46, Glu50 | Ile78, Ile94, Pro79, Arg76 | |
| 11 | –5.2 | Val120, Ser121 | Ile78, Ile94, Ala90, Val93 | |
| 12 | –6.3 | Asn46, Pro79a | Ile78, Ile94, Glu50 | |
| CPFX | –7.3 | Ser121, Val120, Val97, Leu98 | Ile94, Gly119 | Glu50, Ile78, Pro79 |
a
Carbon hydrogen bond. The binding interactions (3D and 2D) of the isolated compounds and CPFX against E. coli DNA gyrase are presented as Supporting Information (Figure S49).