Table 5.
Interactions table between enzyme and inhibitors before and after MD simulations
| Complex | Interactions | |||||
|---|---|---|---|---|---|---|
| Before MD simulation | After MD simulation | |||||
| Residue | Interaction | Distance | Residue | Interaction | Distance | |
| StLpxC-0435 |
HIS265 PHE192 ALA215 LEU18 CYS207 LEU62 LEU62 ILE198 ILE198 THR191 Zn |
H-bond H-bond Pi-Alkyl Pi-Alkyl Pi-Alkyl Pi-Alkyl Pi-Alkyl Pi-Alkyl Alkyl Unfavorable donor–donor Covalent interaction |
2.34 2.08 4.56 5.10 5.33 4.80 4.84 5.34 4.43 1.34 – |
PHE192 PHE192 PHE192 PHE192 LEU62 ILE198 ILE198 ILE198 LEU201 CYS207 CYS207 CYS207 LEU18 ALA215 THR191 HIS238 ZN |
H-bond H-bond H-bond Pi-Pi stacked Alkyl Alkyl Pi-Alkyl Pi-Alkyl Alkyl Alkyl Pi-Sulfur Pi-Alkyl Pi-Alkyl Pi-Alkyl C H-bond C H-bond Covalent interaction |
1.98 1.99 1.88 5.32 4.38 5.15 4.82 4.05 4.74 4.61 5.91 5.40 5.27 4.82 2.61 2.39 – |
| StLpxC-0436 |
PHE192 HIS265 LEU62 LEU62 CYS207 ILE198 LEU18 ALA215 THR191 ZN |
H-bond H-bond Alkyl Pi-Alkyl Pi-Alkyl Pi-Alkyl Pi-Alkyl Pi-Alkyl Unfavorable donor donor Covalent interaction |
2.08 2.34 5.43 4.86 5.33 5.47 4.90 4.41 1.34 - |
– | – | – |
| StLpxC-1812 |
THR191 ASP242 CYS63 PHE192 PHE192 LEU62 LEU62 LEU62 LEU18 CYS214 ALA215 ALA215 CYS207 CYS207 VAL217 ILE198 ILE198 Zn |
H-bond H-bond H-bond H-bond Pi–Pi T C H-bond Pi-Alkyl Pi-Alkyl Pi-Alkyl Pi-Sulfur Pi-Alkyl Alkyl Pi-Alkyl Alkyl Alkyl Alkyl Pi-Alkyl Covalent interaction |
2.11 2.76 2.88 2.33 4.92 2.58 4.71 5.33 4.71 5.62 3.84 4.03 5.21 4.61 5.22 3.66 5.30 – |
LEU62 GLU78 PHE192 LEU62 LEU62 HIS163 LYS239 HIS238 CYS63 CYS63 CYS214 LEU18 ALA215 ALA215 ALA215 ZN |
H-bond H-bond H-bond Pi-Alkyl Pi-Alkyl Pi–Pi stacked Pi-cation C H-bond Pi-Sulfur Pi-Sulfur Alkyl Pi-Alkyl Alkyl Pi-Alkyl Pi-Alkyl Covalent interaction |
2.58 2.99 2.24 4.23 4.75 4.97 4.88 2.90 5.73 5.90 4.46 5.37 3.90 4.03 4.95 – |
| StLpxC-2584 |
PHE192 PHE192 HIS265 ASP242 LEU62 LEU62 ALA215 ALA215 ALA215 CYS214 CYS207 CYS207 VAL217 ILE198 ILE198 LEU18 LEU18 ZN |
H-bond Pi–Pi stacked H-bond H-bond C H-bond Pi-Alkyl Pi-Alkyl Pi-Alkyl Alkyl Pi-Sulfur Pi-Alkyl Alkyl Alkyl Alkyl Pi-Alkyl Pi-Alkyl Pi-Alkyl Unfavorable metal donor |
2.69 4.73 2.40 2.63 2.39 4.74 4.94 3.61 4.06 5.25 5.12 4.86 4.94 3.62 5.19 4.65 5.30 1.72 |
PHE192 PHE192 LEU62 CYS207 CYS207 CYS207 ALA215 LEU201 ILE198 ILE198 GLU78 ASP242 LYS239 ZN |
H-Bond H-Bond Pi-Alkyl Pi-Sulfur Pi-Sulfur Alkyl Pi-Alkyl Alkyl Pi-Alkyl Alkyl Attractive Charge Attractive Charge Pi-sigma Covalent interaction |
2.44 1.85 4.63 5.85 5.71 4.76 4.23 5.29 5.06 4.58 4.27 4.73 2.77 – |
| StLpxC-2545 |
PHE192 PHE192 PHE161 CYS63 LEU18 CYS214 ALA215 ALA215 ALA215 VAL217 CYS207 CYS207 ILE198 ILE198 LEU62 LEU62 ZN ZN |
H-Bond Pi–Pi stacked Pi–Pi T C–H bond Pi-Alkyl Pi-Sulfur Pi-Alkyl Pi-Alkyl Alkyl Alkyl Pi-Alkyl Alkyl Alkyl Pi-Alkyl Pi-Alkyl Pi-Alkyl Metal acceptor Unfavorable metal donor |
3.07 4.89 5.72 2.28 4.68 5.43 5.04 3.73 4.18 5.23 5.14 4.57 3.63 5.21 5.45 4.81 3.38 2.37 |
THR191 THR191 ALA215 ILE198 ILE198 VAL217 PHE212 CYS207 GLU78 HIS79 ZN |
H-Bond H-Bond Pi-Alkyl Pi-Alkyl Alkyl Alkyl Alkyl Pi-Sulfur C H-bond C H-bond VanderWaals |
1.90 1.96 4.57 5.07 4.69 4.99 3.37 5.98 2.80 2.32 – |