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Table 3 Molecular docking value of isolated compounds (1–5) against DNA gyrase B (PDB ID: 6F86)

From: Antibacterial and antioxidant activities of extracts and isolated compounds from the roots extract of Cucumis prophetarum and in silico study on DNA gyrase and human peroxiredoxin 5

Ligands Binding Affinity (kcal/mol) H-bond Residual interactions
Hydrophobic/Pi-Cation Van dar Waals
Compound 1 − 6.4 Glu-50 Pro-79 Asp-73, Asn-46, Ala-47, Arg-76, Gly-77, Ile-78, Gly-81, Ile-94, Arg-136, Thr-165
Compound 2 − 6.7 Gly-77, Thr-165 Glu-50 Asp-73, Ile-78, Ile-94
Compound 3 − 6.9 Gly-77, Asn-46, Thr-165 Asp-73, Ala-47, Asp-49, Glu-50, Gly-75, Arg-76, Ile-78, Pro-79, Ile-94, Arg-136
Compound 4 − 5.6 Asp-73 Ile-78 Asn-46, Ala-47, Glu-50, Arg-76, Gly-77, Pro-79, Ile-94, Thr-165
Compound 5 − 6.5 Asp-73 Ile-78, Pro-79, Ile-94 Asn-46, Ala-47, Glu-50, Arg-76, Gly-77, Arg-136, Thr-165,
Ciprofloxacin − 6.9 Asp-73, Asn-46, Arg-76 Ile-78, Ile-94, Glu-50, Gly-77 Ala-47, Pro-79, Thr-165