Table 3.
System | Cognate docking
|
Noncognate docking
|
|||||||
---|---|---|---|---|---|---|---|---|---|
RMSDnat | docking score | RMSDMD |
|
RMSDnat | docking score | RMSDMD |
|
||
T-1 | 6.73 | −5.5 | 4.27 | 7.99 | −6.2 | 1.95 | −11.53 ± 2.38 | ||
6.94 | −6.5 | 2.29 | 1.28 | −7.3 | 1.50 | −12.54 ± 1.88 | |||
6.41 | −6.3 | 3.27 | 6.18 | −7.3 | 2.46 | ||||
0.85 | −8.2 | 1.43 | −12.04 ± 2.13 | 2.31 | −6.7 | 1.76 | −7.95 ± 0.47 | ||
2.18 | −7.5 | 2.00 | −9.08 ± 3.99 | 6.69 | −5.1 | 4.80 | |||
|
|
|
|||||||
T-2 | 4.54 | −7.5 | 2.51 | 4.83 | −7.4 | 1.75 | −15.43 ± 1.09 | ||
5.88 | −6.5 | 6.75 | 1.89 | −8.0 | 1.07 | −18.51 ± 1.40 | |||
6.10 | −6.9 | 1.35 | −20.30 ± 2.43 | 7.09 | −6.1 | 7.54 | |||
0.81 | −9.7 | 1.69 | −23.25 ± 1.35 | 5.73 | −6.5 | 6.94 | |||
5.86 | −8.1 | 2.69 | 6.19 | −7.3 | 1.26 | −12.73 ± 2.02 | |||
|
|
|
|||||||
T-3 | 7.25 | −7.8 | 2.37 | 6.08 | −7.1 | 2.41 | |||
7.78 | −7.2 | 1.55 | −6.29 ± 1.89 | 5.35 | −7.2 | 2.79 | |||
7.15 | −7.2 | 3.76 | 1.21 | −8.9 | 0.91 | −14.19 ± 1.62 | |||
0.20 | −9.4 | 0.74 | −18.95 ± 1.60 | 5.95 | −7.9 | 1.13 | −10.38 ± 1.52 | ||
6.09 | −8.8 | 1.26 | −8.17 ± 3.09 | 4.93 | −7.6 | 1.66 | −4.82 ± 1.47 | ||
|
|
|
|||||||
T-4 | 5.68 | −7.9 | 4.63 | 5.49 | −8.4 | 2.98 | |||
5.41 | −8.2 | 1.06 | −16.38 ± 2.23 | 6.89 | −7.0 | 1.62 | −3.72 ± 2.02 | ||
6.08 | −7.9 | 2.51 | 6.76 | −7.4 | 4.64 | ||||
0.59 | −8.6 | 0.89 | −15.88 ± 0.52 | 0.68 | −8.2 | 1.55 | −16.41 ± 1.97 | ||
5.14 | −7.9 | 1.45 | −9.57 ± 1.16 | 4.93 | −7.5 | 3.20 | |||
|
|
|
|||||||
X-1 | 8.11 | −7.7 | 2.07 | 6.08 | −6.1 | 3.18 | |||
7.04 | −6.6 | 1.72 | −9.36 ± 2.48 | 7.05 | −6.6 | 3.75 | |||
0.48 | −6.9 | 1.33 | −9.78 ± 2.12 | 5.36 | −6.3 | 2.21 | |||
6.17 | −6.4 | 4.99 | 4.46 | −6.4 | 1.92 | −4.93 ± 2.77 | |||
7.55 | −7.0 | 3.05 | 6.95 | −6.4 | 4.48 |
RMSDnat (Å): RMSD of a docked ligand from its native pose, docking score (kcal/mol): binding affinity predicted by AutoDock Vina. RMSDMD (Å): average ligand RMSD from the initial docked pose during the last 100-ps equilibration MD,