Table 1.
Binding affinities and intermolecular bonds of the top hit Ehretia species phytoconstituents, and the coligand within the KPC-2 protein active site.
| ID | Compound | Phytoconstituent group | Docking score (kcal/mol) | MM-GBSA dG bind ((kcal/mol)) | No. of H-bonds and the participating residues | Other bonds and the participating residues |
|---|---|---|---|---|---|---|
| DB01 | Buddlenol B | Phenolic | -8.89 | -64.42 | 5 (Ser70, Asn132, Asn170, Thr215, Thr216) | π-π stacking (Trp105) |
| DB05 | Ehletianol A | Phenolic | -8.60 | -54.10 | 7 (Asn132, Thr215, Thr235, Thr237, Hie274, Glu2762) | — |
| DB06 | Ehletianol B | Phenolic | -8.66 | -53.48 | 7 (Asn1322, Asn218, Thr2372, Hie274, Glu276) | π-π stacking (His219) |
| DB07 | Ehletianol D | Phenolic | -10.42 | -47.35 | 6 (Ser70, Ser1302, Thr235, Thr2372) | π-π cation (Trp105) |
| DB09 | Caffeic anhydride | Phenolic | -7.47 | -46.25 | 5 (Ser130, Asn1702, Thr235, Thr237) | Salt bridge (Lys234) |
| DB10 | Icariside E5 | Phenolic | -11.13 | -60.39 | 7 (Ser702, Asn132, Asn1702, Hie274, Glu276) | — |
| DB11 | Lithospermic acid B | Phenolic | -10.95 | -79.36 | 4 (Ser70, Thr216, Thr235, Thr237) | π-π stacking (Trp105) |
| DB12 | Methyl rosmarinate | Phenolic | -8.98 | -53.20 | 5 (Ser702, Asn1702, Thr235) | — |
| DB16 | Hyperoside | Flavonoid | -10.71 | -62.84 | 7 (Ser70, Ser1302, Asn1322, Asn170, Thr237) | π-π stacking (Trp1053) |
| DB19 | Quercetin | Flavonoid | -7.53 | -44.79 | 3 (Ser70, Thr2162) | π-π stacking (Trp105) |
| DB28 | Ehretioside B | Glycoside | -8.79 | -48.91 | 3 (Asn132, Asn170, Thr237) | π-cation (Lys234) |
| DB63 | Rutin | Flavonoid | -12.55 | -66.33 | 7 (Ser702, Asn132, Leu167, Thr235, Thr237, Cys238) | π-π stacking (Trp1053) |
| DB64 | Lucenin 2 | Flavonoid | -11.23 | -58.65 | 5 (Ser70, Asn1322, Thr2372) | — |
| DB66 | Riboflavin | Vitamin | -9.61 | -64.63 | 5 (Ser70, Asn170, Thr235, Thr237, Cys238) | — |
| Coligand | Faropenem | Reference | -7.33 | -14.30 | 6 (Ser70, Ser130, Asn132, Thr235, Thr2372) | Salt bridge (Lys73, Lys234); π-cation (Lys73) |
Amino acid residues with numbers (n (a)) represent the total residues involved in the interaction while amino acid residues with superscripts (an) represent the number of bonds participating in the interaction.