sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2007-12-23
| Name: | Genome polyprotein |
|---|---|
| ID: | POLG_HCVBK |
| AC: | P26663 |
| Organism: | Hepatitis C virus genotype 1b |
| Reign: | Viruses |
| TaxID: | 11105 |
| EC Number: | 2.7.7.48 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 40.345 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.341 | 2308.500 |
| % Hydrophobic | % Polar |
|---|---|
| 37.13 | 62.87 |
| According to VolSite | |
| HET Code: | 2PD |
|---|---|
| Formula: | C23H23N4O5S |
| Molecular weight: | 467.518 g/mol |
| DrugBank ID: | DB06974 |
| Buried Surface Area: | 57.49 % |
| Polar Surface area: | 131.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 52.433 | -8.12045 | 52.019 |
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 |
| C18 | CG | PRO- 197 | 3.67 | 0 | Hydrophobic |
| C19 | CD | ARG- 200 | 3.55 | 0 | Hydrophobic |
| C20 | CB | ASP- 318 | 4.16 | 0 | Hydrophobic |
| C22 | CB | CYS- 366 | 3.94 | 0 | Hydrophobic |
| C19 | CB | CYS- 366 | 3.87 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 384 | 3.45 | 0 | Hydrophobic |
| C23 | CE | MET- 414 | 3.86 | 0 | Hydrophobic |
| C2 | CG | MET- 414 | 3.71 | 0 | Hydrophobic |
| C22 | CZ | TYR- 415 | 4.36 | 0 | Hydrophobic |
| C18 | CZ | TYR- 448 | 4.29 | 0 | Hydrophobic |
| C23 | CE1 | TYR- 448 | 3.83 | 0 | Hydrophobic |
| C8 | CB | SER- 556 | 3.77 | 0 | Hydrophobic |
| O30 | O | HOH- 641 | 2.8 | 179.98 | H-Bond (Protein Donor) |
