sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2009-01-07
| Name: | Genome polyprotein |
|---|---|
| ID: | POLG_HCVCO |
| AC: | Q9WMX2 |
| Organism: | Hepatitis C virus genotype 1b |
| Reign: | Viruses |
| TaxID: | 333284 |
| EC Number: | 2.7.7.48 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 14.487 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.270 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.35 | 49.65 |
| According to VolSite | |
| HET Code: | 79Z |
|---|---|
| Formula: | C22H23FN2O5S |
| Molecular weight: | 446.492 g/mol |
| DrugBank ID: | DB07238 |
| Buried Surface Area: | 77.46 % |
| Polar Surface area: | 108.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -16.8266 | -12.766 | 9.52652 |
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 |
| C1 | CE1 | PHE- 193 | 3.64 | 0 | Hydrophobic |
| C3 | CD1 | PHE- 193 | 3.6 | 0 | Hydrophobic |
| C12 | CD | ARG- 200 | 4.24 | 0 | Hydrophobic |
| C14 | CD | ARG- 200 | 3.43 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 204 | 3.52 | 0 | Hydrophobic |
| C13 | SG | CYS- 316 | 3.95 | 0 | Hydrophobic |
| C3 | SG | CYS- 316 | 3.85 | 0 | Hydrophobic |
| F28 | CG1 | VAL- 321 | 4.21 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 321 | 3.66 | 0 | Hydrophobic |
| F28 | CD1 | LEU- 360 | 4 | 0 | Hydrophobic |
| F28 | CB | ILE- 363 | 3.26 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 363 | 3.76 | 0 | Hydrophobic |
| N21 | OG | SER- 365 | 2.83 | 156.17 | H-Bond (Ligand Donor) |
| C4 | CB | SER- 365 | 3.64 | 0 | Hydrophobic |
| C1 | SG | CYS- 366 | 4.4 | 0 | Hydrophobic |
| C13 | SG | CYS- 366 | 3.64 | 0 | Hydrophobic |
| C14 | CB | CYS- 366 | 3.67 | 0 | Hydrophobic |
| C30 | CB | CYS- 366 | 4.08 | 0 | Hydrophobic |
| C12 | CB | CYS- 366 | 4.15 | 0 | Hydrophobic |
| C12 | CB | SER- 368 | 3.81 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 384 | 4.22 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 384 | 4.09 | 0 | Hydrophobic |
| C27 | CB | LEU- 384 | 4.1 | 0 | Hydrophobic |
| C27 | CB | MET- 414 | 4.27 | 0 | Hydrophobic |
| C29 | SD | MET- 414 | 3.82 | 0 | Hydrophobic |
| C27 | CE1 | TYR- 415 | 3.66 | 0 | Hydrophobic |
| C29 | CZ | TYR- 415 | 4.18 | 0 | Hydrophobic |
| C1 | CD1 | TYR- 448 | 3.91 | 0 | Hydrophobic |
| C2 | CE1 | TYR- 448 | 3.46 | 0 | Hydrophobic |
| O31 | O | HOH- 685 | 3.13 | 164.25 | H-Bond (Ligand Donor) |
