Table 4. Ligands that are scored best only in GDP-bound Rab11b (PDB entry 4OJK_A).
| Ligands | Site | Free energy (Kcal/mol) | Interactions |
|---|---|---|---|
| ZINC17465979 | Site 1 | -8.2 | Hydrophobic interactions- ASP19, THR98 Hydrogen bonds- SER20, ASN101, ARG104 |
| ZINC05462670 | Site 1 | -8.1 | Hydrogen bonds- GLY18, SER20, ASN101, ARG104 |
| ZINC05462674 | Site 1 | -8.1 | Hydrogen bonds- GLY18, SER20, ASN101, ARG104 |
| ZINC12672242 | Site 1 | -8.4 | Hydrogen bonds-SER20 |
| ZINC17465983 | Site 1 | -8.1 | Hydrophobic interaction- LEU97 Hydrogen bonds- SER20, ASN101, ARG104 |
| ZINC01668429 | Site 2 | -8 | Hydrogen bonds- GLU103, ASN147, GLU171 |
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. The listed ligands were also reported as hits for the respective target structures while redocking. The ligand structures are shown in S38 Fig. GDP stands for Guanosine-5'-Diphosphate.