Table 3. Binding energies and dissociation constants (Kd) of some known physiological ligands with target protein(s).
| AutoDock v4.2.6 | AutoDock vina | iGEMDOCK v2.1 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| S. No | Protein target | Physiological ligand | Experimental binding constants | B.E.(kcal/mol) | Kd | B.E.(kcal/mol) | Kda | T.E.(kcal/mol) | VDW | HB | EI |
| 1 | Vimentin | Acetate | – | −1.5 | 79.67 mM | −3.0 | 6.45 mM | −39.24 | −23.28 | −11.98 | −3.97 |
| ATP | 14.0 µM (Esue et al., 2006) | −1.26 | 119.56 mM | −7.3 | 4.0 µM | −107.26 | −53.35 | −45.43 | −8.47 | ||
| N-acetyl glucosamine | 55.7 µM (Ise et al., 2017) | −5.05 | 197.38 µM | −6.6 | 15.46 µM | −89.06 | −54.77 | −34.29 | 0 | ||
| 2 | Gelsolin | Calcium | 1.0 µM (Lamb et al., 1993) | −0.84 | 241.61 mM | −1.3 | 108.84 mM | – | – | – | – |
| ATP | 2.4 µM (Szatmári et al., 2018) | −2.31 | 20.28 mM | −6.8 | 9.50 µM | −117.01 | −72.39 | −40.43 | −4.19 | ||
| Phosphatidylinositol (4,5)-bisphosphate | 40.2 µM (Lin et al., 1997) | – | – | −5.9 | 43.43 µM | −113.81 | −84.67 | −27.49 | −1.65 | ||
| Phosphatidylinositol 4- monophosphate | ND | – | – | −7.2 | 4.39 µM | −103.32 | −68.52 | −29.74 | −5.06 | ||
| 3 | Villin | Acetate | ND | −2.24 | 22.69 mM | −2.9 | 6.0 mM | −36.47 | −16.07 | −20.02 | −0.2 |
| Sulfate | ND | −2.79 | 9.06 mM | −3.2 | 4.75 mM | −45.35 | −12.42 | −27.32 | −3.61 | ||
| ATP | ND | −4.1 | 989.87 µM | −7.4 | 3.75 µM | −100.82 | −51.19 | −41.62 | −8.01 | ||
| Phosphatidylinositol (4,5)-bisphosphate | 39.5 µM (Kumar et al., 2004) | – | – | −6.0 | 39.91 µM | −123.84 | −88.58 | −28.72 | −6.55 | ||
| Phosphatidylinositol 4- monophosphate | ND | – | – | −6.8 | 10.02 µM | −104.78 | −92.83 | −8.78 | −3.18 | ||
| 4 | Coronin-1A | Zinc | ND | −0.76 | 275.13 mM | −1.2 | 139.32 mM | – | – | – | – |
| ATP | ND | −3.68 | 2.02 mM | −8.3 | 869.1 nM | −108.04 | −83.02 | −29.21 | 4.2 | ||
| Acetate | ND | −2.64 | 11.69 mM | −2.9 | 6.92 mM | −57.3 | −28.34 | −24.71 | −4.26 | ||
| Sulfate | ND | −2.48 | 15.33 mM | −3.4 | 3.19 mM | −59.23 | −29.6 | −25.45 | −4.18 | ||
| Phosphatidylinositol (4,5)-bisphosphate | 0.64 µMb (Olshina et al., 2015) | – | – | −5.6 | 76.59 µM | −82.84 | −79.34 | −3.5 | 0 | ||
| Phosphatidylinositol 4- monophosphate | ND | – | – | −6.7 | 15.3 µM | −135.26 | −112.19 | −23.89 | 0.81 | ||
| 5 | Thymosin β-4 | ATP | 1.8-22 µM (Carlier et al., 1993) | −1.89 | 41.01 mM | −4.8 | 300.02 µM | −78.74 | −53.85 | −21.79 | −3.1 |
| Calcium | ND | −0.45 | 468.21 mM | −1.0 | 168.72 mM | – | – | – | – | ||
| 6 | Ezrin | Sulfate | ND | −6.68 | 12.74 µM | −3.4 | 3.19 mM | −57.55 | −17.29 | −31.39 | −8.88 |
| ATP | ND | −4.74 | 332.92 µM | −8.6 | 515.45 nM | −114.68 | −56.11 | −51.47 | −7.1 | ||
| Phosphatidylinositol (4,5)-bisphosphate | 52 nM (Bosk et al., 2011) | – | – | −6.9 | 8.5 µM | −122.25 | −78.09 | −37.01 | −7.15 | ||
| 7 | Cofilin | Magnesium | ND | −0.95 | 202.36 mM | −1.3 | 109.84 mM | – | – | – | – |
| ATP | 0.08 µM (Chen & Pollard, 2011) | – | – | −5.8 | 55.7 µM | −105.96 | −72.8 | −31.61 | −1.54 | ||
Notes.
a
Dissociation constants obtained using AutoDock vina have been cited in the text on account of greater consistency to reported experimental values of the ligands for the respective target proteins.
b
As determined for coronin from Plasmodium falciparum
–
No significant binding detected.
- ND
- Experimental binding constants unknown/not determined