Table 2. Ligands that are scored best only in GDP-bound Rab11a (PDB entry 1OIV_A).
| Ligand | Site | Free energy computed by AutoDockVina (Kcal/mol) | Interactions |
|---|---|---|---|
| ZINC00084617 | Site 1 | -8.6 | Hydrogen bonds- ASN 101, TRP 105 Salt bridges—ARG104, GLU108 |
| ZINC01578333 | Site 1 | -8.9 | Hydrogen bonds- ASN101, Salt bridge- ASP19 |
| ZINC13208966 | Site 1 | -8.9 | Hydrophobic interactions- ARG104 Hydrogen bonds- ARG104 |
| ZINC04720972 | Site 1 | -8.6 | Hydrogen bonds-ASN101, TRP105 |
| ZINC11677172 | Site 1 | -8.6 | Hydrophobic interaction- GLU108, Hydrogen bonds- SER20, ARG72 |
| ZINC00393674 | Site 1 | -8.5 | Hydrogen bonds-ASN101, ARG104, GLU108 |
| ZINC01701460 | Site 1 | -8.8 | Hydrogen bond-ASN 101 π-Cation Interaction- ARG72 |
The target sites of ligands in 1OIV_A, 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 S31–S33 Figs. GDP stands for Guanosine-5'-Diphosphate.