Skip to main content

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 (Ã…)

Distance between the protein (Glu220 COOH group) and the ligand thiol group (Ã…)

Distance between C4 of NADPH and the thioester carbonyl carbon of the substrate (Ã…)

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