Table 3.
Docking results of compounds with DNA (PDB ID: 1Z3F).
| Distance (Å) | Nucleic acid | Moiety of ligand | Interactions |
Ki
(nM) |
ΔG ( kcal/mol) | Compound |
| DC1, DC2DG5, DG6 | Phenanthrene S H-S |
π -π stacking π –Sulfur H-bond |
152.16 | -9.19 | P1 | |
| DC1, DC2DG5, DG6 | Phenanthrene | π -π stacking |
118.64 | -9.45 | P2 | |
| DC1, DC2DG5, DG6 | Phenanthrene | π -π stacking |
105.14 | -9.52 | P3 | |
| 3.066 | DC1, DC2DG5, DG6 | S Phenanthrene |
H-bond, π -π stacking |
120.09 | -9.44 | P4 |
| DC1, DC2DG5, DG6 | Phenanthrene | π -π stacking |
71.09 | -9.75 | P5 | |
| DC1, DC2DG5, DG6 | Phenanthrene | π -π stacking |
68.85 | -9.77 | P6 | |
| 2.760 | DC1, DC2DG5, DG6 | S Phenanthrene |
H-bond, π -π stacking |
86.47 | -9.64 | P7 |
| 2.775 2.939 |
DC1, DC2DG5, DG6 | O Phenanthrene |
H-bond, π -π stacking |
110.88 | -9.49 | P8 |
| DC1, DC2DG5, DG6 | Phenanthrene | π –π stacking |
20.23 | -10.50 | P9 | |
| 2.760 | DC1, DC2DG5, DG6, DA3 |
N Phenanthrene |
H-bond, π -π stacking |
25.23 | -10.37 | P10 |
| DC1, DC2DG2, DG6 | Phenanthrene S |
π –π stacking π - Sulfur |
94.52 | -9.58 | P11 | |
| DC1, DC2DG5, DG6, DA3 |
Phenanthrene | π –π stacking |
9.11 | -10.97 | P12 | |
| DC1, DC2DG5, DG6, DA3 |
Phenanthrene | π –π stacking |
52.36 | -9.93 | P13 | |
| DC1, DC2DG5, DG6 | Phenanthrene | π –π stacking |
23.47 | -10.41 | P14 | |
| DC1, DC2DG5, DG6 | Phenanthrene Phenyl CH3-Phenyl |
π –π stacking π – Sigma π --Alkyl |
11.61 | -10.83 | P15 | |
| 3.127 | DC1, DC2DG5, DG6, DA3 |
S Phenanthrene |
H-bond, π -π stacking |
21.89 | -10.45 | P16 |