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
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 |
|---|---|
| A | 100 % |
| B-Factor: | 31.037 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.319 | 236.250 |
| % Hydrophobic | % Polar |
|---|---|
| 57.14 | 42.86 |
| According to VolSite | |
| HET Code: | 1JL |
|---|---|
| Formula: | C20H16NO5S |
| Molecular weight: | 382.410 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.77 % |
| Polar Surface area: | 103.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -24.2106 | 50.9271 | 55.4132 |
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 |
| C15 | CD1 | LEU- 419 | 4.4 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 419 | 3.76 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 419 | 4.04 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 419 | 3.68 | 0 | Hydrophobic |
| C27 | CB | ARG- 422 | 3.39 | 0 | Hydrophobic |
| C2 | CB | MET- 423 | 4.22 | 0 | Hydrophobic |
| C22 | SD | MET- 423 | 3.47 | 0 | Hydrophobic |
| C23 | CE | MET- 423 | 3.76 | 0 | Hydrophobic |
| C27 | CB | MET- 423 | 4.2 | 0 | Hydrophobic |
| O18 | N | SER- 476 | 2.72 | 138.72 | H-Bond (Protein Donor) |
| O19 | N | TYR- 477 | 2.97 | 139.28 | H-Bond (Protein Donor) |
| C25 | CG2 | ILE- 482 | 4.31 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 482 | 3.71 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 485 | 3.74 | 0 | Hydrophobic |
| C24 | CB | ALA- 486 | 3.98 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 489 | 3.85 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 497 | 4.03 | 0 | Hydrophobic |
| C22 | CB | LEU- 497 | 4.29 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 497 | 3.9 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 497 | 3.43 | 0 | Hydrophobic |
| C27 | CD2 | TRP- 528 | 3.95 | 0 | Hydrophobic |
| C4 | CB | TRP- 528 | 3.49 | 0 | Hydrophobic |
