Table 3. The hydrogen bond interactions between the p53 (PDB-id: 3D09) and small molecules - withaferin A and withanone.
Protein | Small molecule | Hydrogen bond interactions | Distance (Å) | Binding energy (Kcal/mol) |
p53 (PDB-id: 3D09) | Withaferin A | Arg (282) NH1-H…O6 | 3.23 | −10.18 |
Tyr (126) O6-H…O | 2.77 | |||
Tyr (126) N-H…O6 | 2.92 | |||
Leu (111) O-H…O1 | 3.13 | |||
Leu (111) N-H…O1 | 3.29 | |||
Asn (268) ND2 (A)-H…O2 | 3.08 | |||
Asn (268) O2-H…OD1(A) | 2.98 | |||
Withanone | Leu (111) O4-H…O | 2.48 | −7.98 | |
Leu (111) O-H…O5 | 3.03 | |||
Leu (111) N-H…O5 | 3.08 | |||
Leu (111) N-H…O6 | 3.36 | |||
Phe (113) O2-H…O | 2.67 | |||
Phe (113) O2-H…N | 3.02 | |||
Phe (113) N-H…O1 | 3.16 |
The symbol (A) denotes the A-conformation of the molecule.