Table 2 The descriptor analysis helped in the identification of the better ligand
From: Bioinformatics in crosslinking chemistry of collagen with selective cross linkers
| Â | Coenzyme Q 10 | Dopaquinone | Embelin | Embelin complex-1 | Embelin complex-2 | Idebenone | 5-O-Methyl embelin | Potassium embelate without K | Vilangin |
|---|---|---|---|---|---|---|---|---|---|
Molecular Physicochemical properties | |||||||||
Logp (Octanol-water partition coefficient) | 10.509 | -2.684 | 4.617 | 4.753 | 5.413 | 4.197 | 4.893 | 2.247 | 9.248 |
TPSA (Polar surface area) | 52.61 | 97.464 | 74.598 | 172.374 | 227.469 | 72.838 | 63.604 | 77.427 | 149.196 |
No. of atoms(Number of nonhydrogen atoms) | 63 | 14 | 21 | 44 | 50 | 24 | 22 | 21 | 43 |
M.wt (Molecular weight) | 863.365 | 195.174 | 294.391 | 626.828 | 710.774 | 338.444 | 308.418 | 293.383 | 600.793 |
No. of ON (Number of hydrogen-bond acceptors [O and N atoms]) | 4 | 5 | 4 | 10 | 16 | 5 | 4 | 4 | 8 |
No. of OHNH (Number of hydrogen-bond donors [OH and NH groups]) | 0 | 3 | 2 | 8 | 2 | 1 | 1 | 1 | 4 |
No. of Violations (Number of Rule of 5 violations) | 2 | 0 | 0 | 2 | 3 | 0 | 0 | 0 | 2 |
No. of rotb (Number of rotatable bonds) | 31 | 3 | 10 | 25 | 27 | 12 | 11 | 10 | 22 |
Volume (Molecular volume) | 937.819 | 166.513 | 295.208 | 617.365 | 651.349 | 338.282 | 312.736 | 292.466 | 594.584 |
Drug likeness | |||||||||
GPCR ligand | -3.37 | -0.21 | -0.42 | -0.49 | -1.18 | -0.22 | -0.41 | -0.14 | -0.34 |
Ion channel modulator | -4.35 | 0.05 | -0.34 | -1.39 | -2.47 | -0.33 | -0.39 | -0.08 | -1.07 |
Kinase inhibitor | -3.93 | -0.84 | -0.05 | -0.88 | -1.55 | -0.21 | -0.05 | -0.16 | -0.51 |
Nulcear receptor ligand | -4.04 | -0.58 | -0.36 | -0.73 | -1.83 | -0.17 | -0.36 | -0.07 | -0.52 |