TABLE 5.
H. pylori protein hydrogen bond analysis with astragalin ligand. This table presents the detailed results of the hydrogen bond interactions between various H. pylori proteins and the astragalin ligand, obtained through molecular docking simulations. The information is organized as follows: Residue Info (Model): Information about the residue and the protein model, including the protein identifier and its origin (PDB or AlphaFold). Atom Donor (Model): Hydrogen donor atom within the protein-ligand complex, including the identification of the protein it comes from. Atom Acceptor (Model): Hydrogen acceptor atom in the astragalin ligand, showing direct interaction with the protein. Hydrogen Atom: Hydrogen atom involved in the bridge, facilitating the bond between donor and acceptor. D.A Distance (Å): Distance between the donor and acceptor atom (D.A), measured in angstroms (Å), indicative of the physical proximity required for an effective hydrogen bridge. D-H.A Distance (Å): Distance between the hydrogen of the donor atom and the acceptor atom (D-H.A), also measured in angstroms, providing details on the spatial orientation of the interaction.
| Residue Info (Model) | Atom Donor (Model) | Atom Acceptor (Model) | Hydrogen Atom | D..A Distance (Å) | D-H..A Distance (Å) |
| ARG 12.A (NikR/AF-O25896- F1) | NE (NikR/AF- O25896-F1) | O11 (astragalin) | HE | 3.238 | 2.310 |
| ARG 12.A (NikR/AF-O25896- F1) | NH2 (NikR/AF- O25896-F1) | O11 (astragalin) | HH21 | 3.193 | 2.278 |
| PHE 13.A (NikR/AF-O25896- F1) | O (NikR/AF- O25896-F1) | O6 (astragalin) | H11 | 3.142 | 2.200 |
| LYS 140.A (NikR/2WVB) | NZ (NikR/2WVB) | O6 (astragalin) | HZ3 | 3.053 | 2.272 |
| LEU 138.A (NikR/2WVB) | O (NikR/2WVB) | O6 (astragalin) | H11 | 3.031 | 2.082 |
| HIS 66.A (HsrA/AF- A0A496FN53-F1) | ND1 (HsrA/AF- A0A496FN53-F1) | O3 (astragalin) | H8 | 3.331 | 2.372 |
| SER 68.A (HsrA/AF- A0A496FN53-F1) | OG (HsrA/AF- A0A496FN53-F1) | O6 (astragalin) | H11 | 2.930 | 2.222 |
| VAL 1111.A (CagA/AF- P55980-F1) | O (CagA/AF- P55980-F1) | O4 (astragalin) | H9 | 2.990 | 2.196 |
| TYR 508.A (CagA/AF- P55980-F1) | O (CagA/AF- P55980-F1) | O9 (astragalin) | H18 | 2.959 | 2.114 |
| ASN 411.P (CagA/4DVY) | OD1 (CagA/4DVY) | O4 (astragalin) | H9 | 3.170 | 2.261 |
| GLU 313.A (urease/AF- P69996-F1) | OE2 (urease/AF- P69996-F1) | O4 (astragalin) | H9 | 2.692 | 1.811 |
| ILE 304.A (urease/AF- P69996-F1) | O (urease/AF- P69996-F1) | O5 (astragalin) | H10 | 3.383 | 2.589 |
| ARG 375.B (urease/1E9Z) | NH1 (urease/1E9Z) | O5 (astragalin) | HH12 | 2.978 | 2.049 |
| ARG 375.B (urease/1E9Z) | NH2 (urease/1E9Z) | O5 (astragalin) | HH22 | 3.276 | 2.462 |
| ASN 189.A (BabA/AF- Q17SX4-F1) | ND2 (BabA/AF- Q17SX4-F1) | O10 (astragalin) | HD22 | 3.134 | 2.347 |
| TYR 102.A (BabA/4ZH0) | O (BabA/4ZH0) | O5 (astragalin) | H10 | 2.967 | 2.144 |
| THR 134.A (BabA/4ZH0) | O (BabA/4ZH0) | O6 (astragalin) | H11 | 3.089 | 2.236 |
| SER 132.A (BabA/4ZH0) | O (BabA/4ZH0) | O9 (astragalin) | H18 | 2.964 | 2.084 |
| ARG 246.A (Flavodoxin/AF- O25342-F1) | NE (Flavodoxin/AF- O25342-F1) | O4 (astragalin) | HE | 2.787 | 1.994 |
| ARG 246.A (Flavodoxin/AF- O25342-F1) | NH2 (Flavodoxin/AF- O25342-F1) | O4 (astragalin) | HH21 | 2.828 | 2.121 |
| ARG 250.A (Flavodoxin/AF- O25342-F1) | NH2 (Flavodoxin/AF- O25342-F1) | O6 (astragalin) | HH21 | 3.212 | 2.357 |
| LEU 285.A (Flavodoxin/AF- O25342-F1) | O (Flavodoxin/AF- O25342-F1) | O11 (astragalin) | H20 | 2.592 | 1.844 |
| ALA 50.A (Flavodoxin/AF- O25342-F1) | O (Flavodoxin/AF- O25342-F1) | O3 (astragalin) | H8 | 3.248 | 2.604 |