Table 3.
Structural analyses of stabilized trajectories following equilibration at 10 ns.
| Analysis | XDH-apo | XDH -ZS025 | XDH -ZS056 | XDH -ZS090 | XDH -ZS093 | XDH -ZS252 |
|---|---|---|---|---|---|---|
| Protein RMSD (nm) | 0.203 ± 0.014 | 0.231 ± 0.009 | 0.207 ± 0.015 | 0.208 ± 0.013 | 0.247 ± 0.01 | 0.204 ± 0.016 |
| Ligand RMSD (nm) | N/A | 0.04 ± 0.008 | 0.087 ± 0.02 | 0.088 ± 0.025 | 0.092 ± 0.025 | 0.086 ± 0.012 |
| Radius of gyration (nm) | 3.216 ± 0.006 | 3.212 ± 0.005 | 3.207 ± 0.007 | 3.21 ± 0.005 | 3.236 ± 0.006 | 3.219 ± 0.006 |
| Solvent accessible surface area (nm2) | 497.8 ± 3.969 | 495.465 ± 4.137 | 490.625 ± 4.593 | 490.129 ± 4.775 | 503.408 ± 4.947 | 492.797 ± 4.726 |
| RMSF (nm) | 0.113 ± 0.056 | 0.11 ± 0.067 | 0.112 ± 0.064 | 0.108 ± 0.052 | 0.111 ± 0.065 | 0.114 ± 0.061 |
| Number of hydrogen bonds | N/A | 5687 ± 1.044 | 3155 ± 0.708 | 2104 ± 0.659 | 0 ± 0 | 4864 ± 0.788 |
| Number of pairs within 0.35 nm | N/A | 31011 ± 1.957 | 15082 ± 2.467 | 4854 ± 1.161 | 3791 ± 0.943 | 12550 ± 1.243 |
N/A, not applicable; RMSD, root mean square deviation of backbone Cα atoms; RMSF, root mean square fluctuation; XDH, xanthine dehydrogenase; ZS025, scutellarein; ZS056, benzyl alpha-D-mannopyranoside; ZS090, elemol; ZS093, diisobutyl phthalate; ZS252, (3R)-hydroxy-beta-ionone.