TABLE 5.
Hydrogen bond distances of protease inhibitors with selected active-site residuesa
| Inhibitor | PDB ID | Hydrogen bond distance(s) (Å)
|
||
|---|---|---|---|---|
| Asp29 | Asp30 | Asp30′ | ||
| GRL-98065 | 1.9/2.4 | 2.4 | 2.5 | |
| DRV | 1S6G | 2.3/2.4 | 2.4 | 2.5 |
| SQV | 1HXB | 1.9 | 2.2 | NP |
| RTV | 1HXW | 2.1 | NP | 2.2 |
| IDV | 1SDT | 2.1 | NP | NP |
| NFV | 1OHR | NP | NP | NP |
| APV | 1HPV | 2.8 | 2.6 | NP |
| LPV | 1MUI | 1.7 | NP | NP |
| ATV | 2AQU | 1.9 | NP | NP |
a
Hydrogen atoms were added and optimized with constraints on heavy atoms using the OPLS2005 force field (MacroModel, version 9.1; Schrödinger, LLC). Hydrogen bond tolerances used were as follows: 3.0 Å for H—A distance; D—H—A angle greater than 90°; and H—A—B angle greater than 60°, where H is the hydrogen atom, A is the acceptor, D is the donor, and B is a neighbor atom bonded to the acceptor. Values for separate interactions are separated by a shill. NP (not present) denotes that a hydrogen bond is not present between the inhibitor and the particular residue. ID, identifier.