Table 3.
Analysis of functional and binding sites of ligands for PLA2-like toxins from Bothrops snakes.
| PDB id | Toxin | RMSD (Å)§ | Roll Angle (°) | MDoS distance (Å) | MDiS distance A (Å) | MDiS distance B (Å) | Binding sites | Inhibitor class | |
|---|---|---|---|---|---|---|---|---|---|
| Toxin + Inhibitor | 3HZW |
BthTX-I BPB |
4.13 | 170 | 13.9 | 9.7 | 6.2 | Hydrophobic channel in monomer A and B | 1 |
| 2OK9 |
PrTX-I BPB |
5.03 | 181 | 15.5 | 4.5 | 5.3 | Hydrophobic channel in monomer A and B | 1 | |
| 1Y4L |
BaspTX-II Suramin |
4.67 | 174 | 14.1 | 4.6 | 4.8 | Hydrophobic channel in monomer A and B | 1 | |
| 6PWH |
MjTX-II Varespladib |
- | 163 | 21.1 | 4.8 | 4.5 | Hydrophobic channel in monomer A and B andMDiS from both monomers | 1, 2 | |
| 3QNL |
PrTX-I Rosmarinic Acid |
4.54 | 173 | 14.5 | 4.8 | 5.2 | Hydrophobic channel entrance and MDiS from monomer B | 1, 2 | |
| 4WTB |
BthTX-I Zinc |
4.22 | 142 | 16.8 | 10.3 | 4.7 | Hydrophobic channel and MDiS from both monomers | 1, 2 | |
| 6DIK |
BthTX-I Chicoric Acid |
4.69 | 180 | 15.4 | 5.0 | 5.1 | Hydrophobic channel entrance and MDiS from monomer B | 1, 2 | |
| 4YU7 |
PrTX-I Caffeic Acid |
5.00 | 177 | 14.9 | 5.0 | 4.7 | MDoS | 2 | |
| 4YZ7 |
PrTX-I Aristolochic Acid |
4.98 | 181 | 14.8 | 4.7 | 4.8 | MDiS from monomer A | 2 | |
| 6MQD |
MjTX-II Rosmarinic Acid |
0.40 | 166 | 19.3 | 4.7 | 4.8 | MDiS from monomer B | 2 | |
| 6CE2 |
MjTX-I Suramin |
4.99 | 175 | 14.8 | 8.6 | 9.4 | Hydrophobic channel in monomer A and B | 3 | |
| 4YV5 |
MjTX-II Suramin |
4.69 | 170 | 14.4 | 5.0 | 4.9 | MDoS and MDiS simultaneously in both monomers | 3 | |
| Toxin + Activator | 3IQ3 |
BthTX-I PEG4000 |
5.13 | 178 | 14.5 | 4.7 | 5.2 | Hydrophobic channel | — |
| 6B84 | MjTX-II | 3.73 | 164 | 13.7 | 4.4 | 4.5 | Hydrophobic channel | — | |
| 6B83 |
MjTX-II Fatty Acid 6 |
4.39 | 169 | 14.4 | 6.4 | 5.2 | Hydrophobic channel | — | |
| 6B81 |
MjTX-II Fatty Acid 8 |
3.77 | 167 | 13.7 | 4.9 | 5.0 | Hydrophobic channel | — | |
| 6B80 |
MjTX-II Fatty Acid 14 |
4.73 | 170 | 14.3 | 4.8 | 5.0 | Hydrophobic channel | — | |
| 1XXS |
MjTX-II Fatty Acid 18 |
4.66 | 170 | 14.8 | 4.4 | 4.7 | Hydrophobic channel | — | |
| 4KF3 |
MjTX-II PEG4000 |
4.80 | 170 | 14.2 | 4.4 | 4.4 | Hydrophobic channel | — | |
| 3MLM |
BnIV Fatty Acid 14 |
4.97 | 179 | 14.7 | 4.6 | 5.4 | Hydrophobic channel | — | |
| 4K06 |
MTX-II PEG4000 |
4.99 | 178 | 14.8 | 5.1 | 4.9 | Hydrophobic channel | — | |
| Inactive Toxin | 2H8I |
BthTX-I PEG400* |
4.15 | 141 | 17.0 | 8.5 | 4.9 | Hydrophobic channel | — |
| 3I3H | BthTX-I | 4.15 | 141 | 17.5 | 9.3 | 4.6 | — | — | |
| 3HZD | BthTX-I | 4.17 | 141 | 17.3 | 11.2 | 4.8 | — | — | |
| 2Q2J | PrTX-I | 4.13 | 141 | 17.4 | 10.9 | 4.9 | — | — | |
| 4K09 | BbTX-II | 4.17 | 142 | 17.4 | 10.8 | 4.5 | — | — | |
| 6MQF |
MjTX-II Aspirin# |
0.44 | 165 | 21.4 | 4.8 | 4.8 | Hydrophobic channel in monomer A and B | — |
§RMSD calculated using MjTX-II/Varespladib as reference structure for superposition.
*Length of PEG400 molecule is not able to activate the toxin.
#Aspirin molecules bind to toxin but do not inhibit the myotoxic effects of MjTX-II.