Putting enzymes on hold
Table 1. Table showing the data obtained from the docking experiment with 10 Cdc14 inhibitors as ligands, followed by the statistics of the initial inhibitor compared to the final inhibitor. The experiment was performed with 20 Placement poses and 5 Refinement poses. The first 26 poses out of a total of 50 are displayed. The homology model with the peptide ligand chain from 5XW5 in its active site was generated to observe substrate recognition in the Cdc14 homolog. The ligand chain was reduced to S- P, and a docking experiment was performed using the induced fit mode, reproducing the original ligand pose (figure 9). The 10 Cdc14 inhibitor molecules were docked in this pocket site, and the results for 50 poses (5 for each inhibitor) were loaded in a table (table 1). The S value (docking score) for each pose is listed, indicating the affinity between the ligand and the receptor. More negative S values imply stronger binding; thus, D7 (mseq 3) has the highest affinity to the active site. The structure of S. cerevisiae Cdc14 was selected as a model due to its high similarity in conserved domains with the target A. alternata protein. Using this homologue enhances prediction accuracy, ensuring that our inhibitor design aligns closely with the functional characteristics of the A. alternata Cdc14 enzyme.
Minimum
Maximum
Trial 1
0.147
0.411
Trial 2
0.137
0.421
Trial 3
0.144
0.441
Average
0.142667
0.424333
Standard Deviation
0.00419
0.012472
Z’
0.822534
Max-Min
0.281667
70
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