sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2013-01-30
| Name: | Genome polyprotein |
|---|---|
| ID: | POLG_HCVJ4 |
| AC: | O92972 |
| Organism: | Hepatitis C virus genotype 1b |
| Reign: | Viruses |
| TaxID: | 420174 |
| EC Number: | 2.7.7.48 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 42.045 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.667 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 60.20 | 39.80 |
| According to VolSite | |
| HET Code: | 1JG |
|---|---|
| Formula: | C11H6BrClNO4S2 |
| Molecular weight: | 395.657 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.96 % |
| Polar Surface area: | 122.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -21.2814 | -23.7351 | -13.9422 |
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 |
| BR1 | CD1 | LEU- 419 | 3.87 | 0 | Hydrophobic |
| S2 | CD1 | LEU- 419 | 4.27 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 419 | 4.42 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 419 | 3.71 | 0 | Hydrophobic |
| BR1 | CB | ARG- 422 | 3.72 | 0 | Hydrophobic |
| BR1 | CG | MET- 423 | 3.52 | 0 | Hydrophobic |
| S2 | SD | MET- 423 | 3.82 | 0 | Hydrophobic |
| CL1 | CE | MET- 423 | 3.77 | 0 | Hydrophobic |
| O19 | N | SER- 476 | 2.71 | 146.56 | H-Bond (Protein Donor) |
| O18 | N | TYR- 477 | 3.01 | 152.39 | H-Bond (Protein Donor) |
| C13 | CD1 | ILE- 482 | 4.12 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 497 | 4.25 | 0 | Hydrophobic |
| CL1 | CB | LEU- 497 | 3.51 | 0 | Hydrophobic |
| CL1 | CB | ARG- 498 | 4.34 | 0 | Hydrophobic |
| BR1 | CD2 | TRP- 528 | 3.99 | 0 | Hydrophobic |
| S2 | CB | TRP- 528 | 4.4 | 0 | Hydrophobic |
