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Table 3 The docking scores, interaction energies and binding affinity of the substrate obtained from the MOE-DOCK 2008.10 and the ASEDock simulation

From: Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases

Ligand Molecular weight ASEDock Score MOE-Dock Score Eint (Kcal mol-1) Affinity (pKi) Distance between the protein (Tyr176 OH group) and the ligand thioester oxygen atom (Å) Distance between the protein (Glu220 COOH group) and the ligand thiol group (Å) Distance between C4 of NADPH and the thioester carbonyl carbon of the substrate (Å)
Alamethicin 612 -76.6624 -26.726 -43.399 14.776 2.33 3.52 4.13
Trichotoxin 477 -82.4472 -17.826 -32.511 12.817 2.59 3.35 3.35
Antiamoebin 564 -59.8066 -13.566 -34.452 14.467 2.11 3.65 3.71
Chryospermin 605 -77.2101 -25.093 -33.944 14.927 2.60 2.72 3.93
Gramicidin 677 -86.4472 -18.896 -50.249 17.066 3.06 3.70 3.86