Table 1. Experimental and theoretical details of monomeric BLG binding sites.
| Ligand | Octanoic acid | Decanoic acid | Lauric acid | Myristic acid | Palmitic acid | Bromo decanoic | Stearic acid | Oleic acid | Linoleic acid | Retinol | Retinoic acid | Vitamin D3a | DDM |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MW | 144.2 | 172.2 | 200.3 | 228.3 | 256.4 | 279.2 | 284.8 | 282.4 | 280.4 | 286.4 | 300.4 | 384.6 | 510.6 |
| Ligand-protein contactsb | 8 / 0 | 23 / 0 | 16 / 0 | 21 / 0 | 21 / 2 | 15 / 0 | 19 / 0 | 28 / 1 | 19 / 0 | 19/1 | 23 / 0 | 23 / 0 | 11 / 1 |
| Exp. binding energy kcal mol-1 | -5.5 | -5.1 | -7.13 | -8.0 | -8.6 | NA | NA | -8.0 | -7.9 | -9.2 | NA | -11.3 | NA |
| Rigid binding energyc kcal mol-1 | -5.0 | -5.3 | -5.3 | -4.6 | -4.4 | -4.6 | -4.9 | -4.9 | -4.9 | -5.5 | -6.1 | -6.3 | -5.7 |
| Binding energy with 5 flexible residuesd kcal mol-1 | -6.0 | -6.4 | -6.8 | -7.0 | -7.2 | -6.6 | -7.4 | -7.6 | -7.6 | -6.4 | -8.5 | -6.1 | -8.4 |
| Binding energy with 7 flexible residuese kcal mol-1 | -6.0 | -6.6 | -7.1 | -7.1 | 7.3 | -6.7 | -7.6 | -7.9 | -8.0 | -7.3 | -9.3 | -9.1 | -7.9 |
| Isoform | B | B | B | B | B | A | B | B | B | B | B | B | B |
| PDB | 3NQ9[6] | 3NQ3 [6] | 3UEU [41] | 3UEV [41] | 3UEW [41] | 1BSO [45] | 3UEX [41] | 4DQ3f | 4DQ4 g | 1GX8 [3] | 1GX9 [3] | 2GJ5 [5] | 2R56 [46] |
a Data for binding to the monomer.
b As determined by ligplot from XRD structures. Can also be obtained from the PDBSUM website. First number is apolar contacts, second is polar contacts.
c Receptor kept rigid in the original 2BLG conformation.
d Energies calculated from docking to 2BLG with residues L46, L54, I56, I71 and I84 set as flexible.
e Docking to 2BLG with residues L46, L54, I56, I71, I84, F105 and M107 set as flexible.
f Superseeds 3QZK, to be published.g Superseeds 3QZJ, to be published.
NA stands for Not Available
Binding energies in bold correspond to dockings to site C, the only site found in those cases. All others are dockings to Site A.