Table 3. Molecular docking of validation systems.
| rmsd values (Å) | ||||||||
| Glide | GOLD | Autodock | DOCK | |||||
| PDB code | topa | bestb | top | best | top | best | top | best |
| 1Q9Q | 6.5 | 3.7 (15) | 6.8 | 4.3 (2) | 6.3 | 3.7 (27) | 9.8 | 5.7 (7) |
| 1Q9T | 4.8 | 1.5 (7) | 3.4 | 1.0 (5) | 7.3 | 1.9 (3) | 5.0 | 2.0 (4) |
| 3HZK | 4.9 | 1.3 (12) | 1.6 | 1.5 (7) | 3.5 | 3.4 (10) | 4.6 | 1.3 (11) |
| 3HZV | 5.0 | 3.0 (4) | 1.1 | 1.1 (1) | 6.6 | 3.1 (81) | -c | -c |
| 3HZY | 8.4 | 1.2 (11) | 1.5 | 1.2 (4) | 8.6 | 3.2 (48) | 8.1 | 6.3 (3) |
| 3OKK | 6.6 | 1.0 (11) | 1.2 | 1.2 (1) | 1.9 | 1.9 (1) | 5.5 | 3.6 (11) |
| 3OKL | 5.8 | 3.3 (15) | 6.6 | 0.8 (2) | 3.6 | 1.5 (2) | 5.5 | 4.6 (6) |
| 3OKN | 8.2 | 1.7 (11) | 3.0 | 1.3 (8) | 7.5 | 4.1 (30) | 6.4 | 6.4 (1) |
| 3OKO | 7.1 | 2.1 (62) | 6.2 | 3.5 (58) | 4.5 | 3.8 (46) | -c | -c |
| Mean±S.D. | 6.4±1.4 | 2.1±1.0 | 3.5±2.4 | 1.8±1.2 | 5.5±2.2 | 3.0±0.9 | 6.4±1.9 | 4.3±2.1 |
a
Pose ranked first by molecular docking program.
b
Pose which gave the best RMSD value compared to the crystallographic binding mode. The docking rank is shown in parentheses.
c
No ligand poses were obtained following the docking procedure.