Table 1 Docking scores and interactions for all NNI binding sites of hits structure against polymerase receptor with glide program using extra precision mode (hits with asterisk were selected for the molecular dynamics stage).
| NNI Site | XP score | Pi interactions | Salt bridges | HB | Compound |
|---|---|---|---|---|---|
| Palm region | -8.5195 | TYR415 (π-π) | ARG394 |
ARG386 TYR415 | DB05039* |
| Palm region | -8.27362 | - | - |
GLN446 SER368 | DB01940* |
| Palm region | -8.07386 | - |
LYS155 ASP220 |
CYS366 SER367 ARG158 | DB00560* |
| Palm region | -7.11021 | - | - |
SER368 CYS366 GLN446 | DB04118 |
| Palm region | -7.0822 | - | ARG394 |
SER368 TYR448 | DB04142* |
| Palm region | -7.37393 | - | - |
ASP318 TYR448 ASN291 | 3D5M ligand* |
| Palm region | -6.93098 | - | - | TYR448 | 2JC1 ligand* |
| Palm region | -6.5971 | - | - | CYS366 | DB01203 |
| Palm region | -4.64441 | TYR415 (π-π) | ASP318 |
GLN446 ASN316 | DB01888 |
| Thumb II | -7.80905 | HIS475 (π-π) |
ARG501 SER476 | 3FRZ ligand* | |
| Thumb II | -6.9871 | - | - | LEU497 | DB00450 |
| Thumb II | -6.28764 | HIS475 (π-π) | - | SER476 | DB04859 |
| Thumb II | -6.01285 | - | - | SER476 | DB00481 |
| Thumb II | -5.82026 | - |
LYS533 ARG501 | TYR477 | DB04205* |
| Thumb II | -4.39536 | TRP528 (π-π) (2) | - |
ARG501 LEU474 SER473 | DB01087* |
| Thumb II | -3.17019 | TRP528 (σ-π) | - |
ARG501 LEU474 | DB00816* |