Table 2.
Docking results for PpIX molecule inside HSA (1AO6.pdb) showing detailed analysis of the ligand binding sites, protein-ligand interaction energy and major residues involved in hydrogen bonding and hydrophobic interactions. Computational data obtained using the CLC DDWB program [23] and BIOVIA DS Visualizer software [24].
| Binding Sites in HSA | PpIX-HSA Complexes | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Site | Volume (Å3) | Radius (Å) | Location | Domain | Subdomain | α-Helix | Energy (a.u.) a | No. of H-bonds | Common Interacting Residues with PpIX |
| 1 | 787.46 | 15 | Core | I | B | h1, h2, h3, h4 |
−73.55 | 4 (6) b | Arg 117, Tyr 138, Ile 142, His 146, Phe 149, Phe 157, Tyr 161, Arg 186 |
| 2 | 420.35 | 13 | Core | I II III |
B A B A |
h4 h1, h2 h3 h3, h4 |
−70.34 | 3 (5) b | Ala 191, Ala 194, Lys 195, Leu 198, Trp 214, Arg 218, Val 343, Lys 436, Lys 444, Pro 447, Cys 448, Asp 451, Tyr 452, Val 455 |
| 3 | 165.38 | 11 | Surface | II III |
A B A |
h1, h2 h2, h3 h5, h6 |
−11.42 | 0 (2) b | Phe 206, Arg 209, Ala 210, Lys 351 |
| 4 | 146.94 | 10 | Surface | I | A B |
h2, h3 h2, h3 |
−48.25 | 2 (4) b | Glu 17, Ala 21, Ala 158, Lys 159, Lys 162 |
| 5 | 65.02 | 10 | Surface | III | A B |
h1, h2 h2, h3 |
−44.90 | 2 (4) b | Leu 394, Leu 398, Ala 406, Arg 410, Lys 413, Thr 540, Lys 541 |
| 6 | 52.22 | 10 | Surface | III | B | h1, h2 | −33.56 | 1 (3) b | Pro 421, His 510, Thr 506, Phe 509, His 510, Lys 524, Ala 528 |
| 7 | 52.22 | 10 | Surface | III | A | h2, h5, h6 | −49.05 | 2 (4) b | Met 87, Gln 32, Gln 33, Lys 466 |
a The unit of protein-ligand interaction energy is presented in arbitrary units (a.u.); the lower the value, the better the binding affinity; b including intramolecular H-bonds.