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
2013-03-26
| 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: | 70.909 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.787 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 60.29 | 39.71 |
| According to VolSite | |
| HET Code: | 1ML |
|---|---|
| Formula: | C32H35N2O6 |
| Molecular weight: | 543.630 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 46.71 % |
| Polar Surface area: | 108 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -25.1184 | -22.5455 | -17.8357 |
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 |
| C23 | CD1 | LEU- 419 | 4.34 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 419 | 4.41 | 0 | Hydrophobic |
| C02 | CD1 | LEU- 419 | 4.14 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 419 | 3.73 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 419 | 4.02 | 0 | Hydrophobic |
| C29 | CB | ARG- 422 | 3.52 | 0 | Hydrophobic |
| C29 | CB | MET- 423 | 4.35 | 0 | Hydrophobic |
| C24 | CB | HIS- 475 | 4.27 | 0 | Hydrophobic |
| O16 | N | SER- 476 | 2.88 | 141.51 | H-Bond (Protein Donor) |
| O15 | N | TYR- 477 | 3.16 | 146.6 | H-Bond (Protein Donor) |
| C25 | CE1 | TYR- 477 | 3.84 | 0 | Hydrophobic |
| C02 | CD1 | ILE- 482 | 3.76 | 0 | Hydrophobic |
| C08 | CG2 | ILE- 482 | 3.56 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 485 | 4.44 | 0 | Hydrophobic |
| C10 | CB | ALA- 486 | 3.9 | 0 | Hydrophobic |
| C12 | CB | ALA- 486 | 4.31 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 489 | 4.44 | 0 | Hydrophobic |
| C38 | CB | LEU- 489 | 3.9 | 0 | Hydrophobic |
| C37 | CB | LEU- 489 | 3.76 | 0 | Hydrophobic |
| C35 | CB | ARG- 490 | 3.83 | 0 | Hydrophobic |
| C38 | CB | PRO- 496 | 3.99 | 0 | Hydrophobic |
| C05 | CD2 | LEU- 497 | 3.67 | 0 | Hydrophobic |
| C26 | CB | TRP- 528 | 3.75 | 0 | Hydrophobic |
| C29 | CD2 | TRP- 528 | 3.94 | 0 | Hydrophobic |
| C27 | CE3 | TRP- 528 | 3.8 | 0 | Hydrophobic |
