sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2014-07-30
| Name: | Toll-like receptor 8 |
|---|---|
| ID: | TLR8_HUMAN |
| AC: | Q9NR97 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 58 % |
| B | 42 % |
| B-Factor: | 24.751 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.065 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.66 | 42.34 |
| According to VolSite | |
| HET Code: | URI |
|---|---|
| Formula: | C9H12N2O6 |
| Molecular weight: | 244.201 g/mol |
| DrugBank ID: | DB02745 |
| Buried Surface Area: | 74.42 % |
| Polar Surface area: | 119.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 20.7437 | 21.0887 | 37.8291 |
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 |
| C5' | CZ | TYR- 348 | 3.53 | 0 | Hydrophobic |
| C4' | CE2 | TYR- 348 | 3.56 | 0 | Hydrophobic |
| O3' | N | GLY- 351 | 2.94 | 166.28 | H-Bond (Protein Donor) |
| C1' | CG1 | VAL- 378 | 3.88 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 378 | 4.11 | 0 | Hydrophobic |
| C1' | CE2 | PHE- 405 | 4.3 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 405 | 4.36 | 0 | Hydrophobic |
| O4 | NE | ARG- 429 | 3.04 | 155.2 | H-Bond (Protein Donor) |
| O4 | NH2 | ARG- 429 | 3.23 | 142.06 | H-Bond (Protein Donor) |
| N3 | OD2 | ASP- 543 | 2.79 | 169.6 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 545 | 3.03 | 144.12 | H-Bond (Ligand Donor) |
| C5' | CB | VAL- 573 | 4.49 | 0 | Hydrophobic |
| C5' | CG2 | THR- 574 | 4.09 | 0 | Hydrophobic |
| C3' | CG2 | THR- 574 | 3.85 | 0 | Hydrophobic |
| O5' | N | THR- 574 | 3.11 | 150.67 | H-Bond (Protein Donor) |
