Table 3.
Distances between heteroatoms in FPR1 agonists and carbonyl carbon atoms in nearest residues of the FPR1 binding site for docking poses and molecular dynamics (MD) trajectories for ligand–receptor complexes
| Compound | Position of the atoms in the ligand–receptor complex | Distance (Å)
|
|
|---|---|---|---|
| Docking pose | MD trajectorya | ||
| AG-11/03 | SCH3 sulfur – Ala264 | 4.80 | 5.0±0.9 |
| OCH3 oxygen – Leu198 | 4.66 | 4.9±1.0 | |
| Sulfur – Gly202 | 5.86 | 5.6±1.1 | |
| AG-11/05 | OCH3 oxygen (ester) – Val160 | 5.90 | 6.1±1.0 |
| OCH3 oxygen (attached to benzimidazole) – Leu198 | 3.78 | 4.1±0.8 | |
| Sulfur – Ala261 | 4.42 | 4.6±0.9 | |
| AG-11/10 | OCH3 oxygen – Cys98 | 3.85 | 4.0±0.7 |
| CH3CONH nitrogen – Leu198 | 4.28 | 4.1±0.8 | |
| Sulfur – Val160 | 6.70 | 6.3±1.0 | |
a
The ligand–receptor complexes were heated to 310 K for 20 ps, structural data were collected for the next 2 ns at 310 K, and the MD trajectories obtained by HyperChem were analyzed, as described under Materials and methods. Average distances are indicated with their standard deviations over the MD trajectory