Table 2.
Binding Pocket Features – AgamOBP1 and AgamOBP47.
| Main binding pocket (Active site) | AgamOBP1 | AgamOBP47 |
|---|---|---|
| Area (Solvent accessible surface - AS) Å2 | 288.917 | 765.38 |
| Area (Molecular surface - MS) Å2 | 597.09 | 1318.58 |
| Volume (Solvent accessible surface - AS) Å3 | 170.011 | 664.812 |
| Volume (Molecular surface - MS) Å3 | 768.1 | 2050.87 |
| Pocket length (Å) | 329.18 | 651.82 |
| Number of mouth openings | 2 | 3 |
| Mouth area (Solvent accessible surface - AS) Å2 | 8.46 | 150.314 |
| Mouth area (Molecular surface - MS) Å2 | 57.96 | 366.42 |
| Mouth Length (Solvent accessible surface - AS) Å | 26.47 | 143.308 |
| Mouth Length (Molecular surface - MS) Å | 44.93 | 168.99 |
| Number of binding pocket residues/whole protein | 31/125, (25%) | 60/173, (35%) |
| Binding pocket residues - Hydrophobic | 23(74%) | 39 (65%) |
| Binding pocket residues - Hydrophilic | 2 (6.5%) | 13 (21.6%) |
| Binding pocket residues - Positive | 4 (13%) | 5(8.3%) |
| Binding pocket residues - Negative | 2 (6.5%) | 3 (5%) |
| Feasible positions to mutate (KINARI MUTAGEN) | 13/31, (42%) | 27/60, (45%) |
| Number of residues that gave stable mutants (PoPMuSiC) | 6/31, (19%) | 18/60, (30%) |
| Residues that gave stable mutants - Hydrophobic | 2 (33.3%) | 7 (39.9%) |
| Residues that gave stable mutants - Hydrophilic | 1(16.6%) | 5 (27.8%) |
| Residues that gave stable mutants - Positive | 2 (33.3%) | 3 (16.7) |
| Residues that gave stable mutants - Negative | 1 (16.0%) | 3 (16.7%) |
| Total number of stable mutants | 28 | 79 |
| Stable mutants - when a new residue is Hydrophobic | 18 (64.3) | 49 (62%) |
| Stable mutants - when a new residue is Hydrophilic | 5(17.9%) | 19 (24%) |
| Stable mutants - when a new residue is Positive | 4 (14.2%) | 7 (8.8%) |
| Stable mutants - when a new residue is Negative | 1 (3.6) | 4 (5%) |
| Total number of mutant proteins with higher binding affinities than WT after docking screening with drug ligands | 18 | 0 |
| Mutant proteins with higher binding affinities than WT after docking screening - Hydrophobic | 11 | 0 |
| Mutant proteins with higher binding affinities than WT after docking screening - Hydrophilic | 4 | 0 |
| Mutant proteins with higher binding affinities than WT after docking screening - Positive | 3 | 0 |
| Mutant proteins with higher binding affinities than WT after docking screening - Negative | 0 | 0 |
| Å = Angstrom |