Table 3. Ligands that are scored best only in GNP-bound conformations of Rab11a.
| Ligands | Targets | Site | Free energy computed by AutoDockVina (Kcal/mol) | Interactions |
|---|---|---|---|---|
| ZINC04773602 | 1YZK_A | Site 2 | -8 | Hydrophobic interactions- LEU106, LEU109, ARG110, VAL118, ILE119, ASN146, LEU148, GLU171, ILE175 Hydrogen bond- ILE119 |
| ZINC15952559 | 4C4P_A | Site 2 | -8.3 | Hydrogen bonds-ILE117, ILE119, SER149 |
| ZINC11677178 | 4C4P_A | Site 2 | -8 | Hydrophobic interactions- VAL118, GLU171 Hydrogen bonds- ASN116, ILE117, SER149 |
| ZINC12671898 | 4C4P_A | Site 2 | -8 | Hydrophobic interactions- LEU106, ARG110,ILE119 Hydrogen bonds- ILE119, ASN146 Salt bridge- ARG110 |
| ZINC17353914 | 4UJ5_B | Site 1 | -8.2 | Hydrophobic interactions- ASP19, LEU70 Hydrogen bonds- SER20, GLU108 Salt bridge- GLU108 |
| ZINC01573829 | 1YZK_A | Site 2 | -8.3 | Hydrogen bonds- ILE119, GLY147 |
| 4C4P_A | Site 2 | -8 | Hydrogen bonds- SER115 | |
| ZINC01577889 | 1YZK_A | Site 2 | -8.4 | Hydrogen bond- GLY147 |
| ZINC29590275 | 4UJ5_B | Site 1 | -8 | Hydrogen bond-TRP105, GLU108 |
| ZINC01726776 | 1YZK_A | Site 2 | -8.1 | Hydrogen bond- ILE117 |
The target sites of ligands, their free energy of binding and their interactions with Rab11 that are observed using protein-ligand interaction profiler (PLIP) are listed. Target structures for which the ligands scored best are indicated in bold. The listed ligands were also reported as hits for the respective target structures while redocking. The ligand structures are shown in S34–S37 Figs. GNP stands for Phosphoaminophosphonic acid-guanylate ester.