sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2013-10-16
| Name: | Thioredoxin reductase |
|---|---|
| ID: | C4LW95_ENTHI |
| AC: | C4LW95 |
| Organism: | Entamoeba histolytica |
| Reign: | Eukaryota |
| TaxID: | 5759 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 9 % |
| B | 91 % |
| B-Factor: | 35.387 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.407 | 2099.250 |
| % Hydrophobic | % Polar |
|---|---|
| 35.37 | 64.63 |
| According to VolSite | |
| HET Code: | NDP |
|---|---|
| Formula: | C21H26N7O17P3 |
| Molecular weight: | 741.389 g/mol |
| DrugBank ID: | DB02338 |
| Buried Surface Area: | 54.51 % |
| Polar Surface area: | 404.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -13.6804 | 20.7314 | -26.4643 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C3D | CB | ASP- 162 | 4.18 | 0 | Hydrophobic |
| O3D | OD2 | ASP- 162 | 3.02 | 138.95 | H-Bond (Ligand Donor) |
| O1N | N | ALA- 163 | 3.08 | 161.19 | H-Bond (Protein Donor) |
| O2B | NE | ARG- 183 | 3.43 | 147.34 | H-Bond (Protein Donor) |
| O1X | NE | ARG- 183 | 3.08 | 147.93 | H-Bond (Protein Donor) |
| O3X | NH2 | ARG- 183 | 3.16 | 162.1 | H-Bond (Protein Donor) |
| O1X | CZ | ARG- 183 | 3.91 | 0 | Ionic (Protein Cationic) |
| DuAr | CZ | ARG- 183 | 3.68 | 167.18 | Pi/Cation |
| C5B | CD | ARG- 188 | 4.41 | 0 | Hydrophobic |
| C3B | CD | ARG- 188 | 3.67 | 0 | Hydrophobic |
| O2X | CZ | ARG- 188 | 3.43 | 0 | Ionic (Protein Cationic) |
| O3X | CZ | ARG- 188 | 3.82 | 0 | Ionic (Protein Cationic) |
| C1B | CB | ILE- 246 | 4.27 | 0 | Hydrophobic |
| O1A | NH2 | ARG- 291 | 2.85 | 162.55 | H-Bond (Protein Donor) |
| O1A | NH1 | ARG- 291 | 3.28 | 136.44 | H-Bond (Protein Donor) |
| O3 | NH1 | ARG- 291 | 3.48 | 124.86 | H-Bond (Protein Donor) |
| O1A | CZ | ARG- 291 | 3.51 | 0 | Ionic (Protein Cationic) |
