Table 2. Characterization of the NMR structures of the analogues studied by NMR.
ID# | NOE distance restraints |
Angle restraints *** |
CYANA Target function** |
Backbone RMSD (Å) |
Overall RMSD (Å) |
CFF91 energies (Kcal/mol) |
Residual restraint violations on | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Total energy |
Van der Waals |
Electro- static |
Distances | Dihedral Angles | ||||||||
No. ≥ 0.1 Å |
Max (Å) |
No. ≥ 1.5 deg |
Max (deg) |
|||||||||
1 | 116 | 22 | 0.001 | 0.65 ± 0.12 | 1.39 ± 0.21 | 192.7±18 | 100.5 ± 3 | 30.2 ± 2 | 0.1 ± 0.1 | 0.04 ± 0.03 | 0 ± 0 | 0 ± 0 |
3 | 163 | 18 | 0.08 | 0.18 ± 0.09 | 0.62 ± 0.12 | 214.3 ± 4 | 142.7± 2 | 71.6 ± 3 | 0.9 ± 0.1 | 0.12 ± 0.04 | 0 ± 0 | 0 ± 0 |
18 | 110 | 16 | 0.08 | 0.13 ± 0.04 | 0.72 ± 0.15 | 178.2 ± 2 | 132.5 ± 2 | 45.7 ± 1 | 0.8 ± 0.0 | 0.09 ± 0.00 | 0.9 ± 0 | 0.9 ± 0.04 |
19 | 88 | 24 | 0.11 | 0.72 ± 0.20 | 1.12 ± 0.15 | 185.5 ± 6 | 137.2 ± 6 | 48.3 ± 8 | 1.0 ± 0.2 | 0.15 ± 0.06 | 0.5 ± 0.5 | 0.4 ± 0.4 |
21 | 111 | 29 | 0.015 | 0.17 ± 0.07 | 0.79 ± 0.21 | 193.2 ± 4 | 143.8 ± 2 | 49.5 ± 2 | 0.3 ± 0.1 | 0.50 ± 0.07 | 0 ± 0 | 0 ± 0.04 |
The bundle of 20 conformers with the lowest residual target function was used to represent the NMR structures of each analogue.
The target function is zero only if all the experimental distance and torsion angle constraints are fulfilled and all non-bonded atom pairs satisfy a check for the absence of steric overlap. The target function is proportional to the sum of the square of the difference between calculated distance and isolated constraint or van der Waals restraints and similarly isolated angular restraints are included in the target function. For the exact definition see reference.42
Meaningful NOE distance restraints may include intra-residual and sequential NOEs.42