Table 1 Binding energies, amino acid residues, binding distances and types of interaction among ligand and protein molecules
Name of protein (receptor) | PDB ID | Ligand | Binding energy ΔG | Amino acid residues | Distances A° | Type of interaction |
|---|---|---|---|---|---|---|
Human Caspase-I | 6BZ9 | VC | − 7.2 kcal/mol | LYS A:134 | 2.90 | Conventional H-Bond |
CYS A: 136 | 3.99 | Pi-alkyl | ||||
VAL A: 133 | 4.20 | Pi-alkyl | ||||
ILE A: 152 | 5.10 | Pi-alkyl | ||||
TYR A: 153 | 4.75 | Vander Waal | ||||
LEU A: 196 | 3.40 | Vander Waal | ||||
LEU A: 196 | 5.44 | Pi-Alkyl | ||||
LEU A: 135 | 5.48 | Alkyl | ||||
ARG A: 163 | 4.86 | Vander Waal | ||||
Human COX-II | 1CX2 | VC | − 8.0 kcal/mol | GLN A: 192 | 3.79 | C–H bond |
GLY A: 354 | 3.73 | C–H bond | ||||
HIS A: 351 | 3.59 | C–H bond | ||||
HIS A: 356 | 4.55, 3.85 | Pi-Cation | ||||
GLU A: 281 | 3.31 | C–H bond | ||||
HIS A: 356, LYS A: 97 | 5.60, 5.24 | Unfavourable cationic-cationic | ||||
Human NFkB | 1A3Q | VC | − 8.1 kcal/mol | ASP A: 319 | 4.10 | Pi-anion |
ASP A: 319 | 5.34 | C–H bond | ||||
LYS A: 229 | 3.69 | Pi-alkyl | ||||
GLU A: 71 | 3.54 | C–H bond | ||||
ALA A: 68 | 5.38 | Pi-alkyl | ||||
Human TNF-α | 1CA4 | VC | − 7.0 kcal/mol | ARG A: 363 | 3.23 | H–bond |
LYS A: 364 | 3.07 | H–bond | ||||
LYS A: 364 | 5.13 | Alkyl | ||||
TRP A: 356 | 3.14 | H–bond | ||||
LYS A: 357 | 2.85 | H–bond | ||||
ILE A: 376 | 4.98 | Alkyl | ||||
ILE A: 373 | 5.31, 5.16 | Alkyl | ||||
ILE A: 358 | 3.36 | C–H bond |