sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2013-03-24
| 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: | 87.572 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.777 | 411.750 |
| % Hydrophobic | % Polar |
|---|---|
| 62.30 | 37.70 |
| According to VolSite | |
| HET Code: | 1NV |
|---|---|
| Formula: | C23H13F6N3O3 |
| Molecular weight: | 493.358 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.74 % |
| Polar Surface area: | 84.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -23.2199 | -23.0949 | -14.4703 |
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 |
| F29 | CD2 | LEU- 419 | 4.37 | 0 | Hydrophobic |
| F30 | CD2 | LEU- 419 | 4.22 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 419 | 3.57 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 419 | 3.8 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 419 | 3.96 | 0 | Hydrophobic |
| C3 | CB | ARG- 422 | 4.37 | 0 | Hydrophobic |
| F28 | CD | ARG- 422 | 3.62 | 0 | Hydrophobic |
| C4 | CB | MET- 423 | 4.28 | 0 | Hydrophobic |
| F28 | CB | MET- 423 | 4.44 | 0 | Hydrophobic |
| F29 | SD | MET- 423 | 3.27 | 0 | Hydrophobic |
| F19 | CE | MET- 423 | 3.45 | 0 | Hydrophobic |
| F31 | CB | HIS- 475 | 3.26 | 0 | Hydrophobic |
| N8 | N | SER- 476 | 2.77 | 148.45 | H-Bond (Protein Donor) |
| O18 | N | TYR- 477 | 3.26 | 127.07 | H-Bond (Protein Donor) |
| F31 | CE1 | TYR- 477 | 3.66 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 482 | 4.39 | 0 | Hydrophobic |
| F30 | CG2 | ILE- 482 | 4.36 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 482 | 3.71 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 482 | 3.78 | 0 | Hydrophobic |
| F30 | CG1 | VAL- 485 | 3.48 | 0 | Hydrophobic |
| F19 | CB | ALA- 486 | 4.39 | 0 | Hydrophobic |
| F30 | CB | ALA- 486 | 4.07 | 0 | Hydrophobic |
| C25 | CB | ALA- 486 | 4.44 | 0 | Hydrophobic |
| F19 | CD1 | LEU- 489 | 3.25 | 0 | Hydrophobic |
| F29 | CB | LEU- 497 | 3.88 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 497 | 3.58 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 497 | 3.7 | 0 | Hydrophobic |
| O34 | N | LEU- 497 | 2.84 | 155.78 | H-Bond (Protein Donor) |
| F28 | CD2 | TRP- 528 | 3.8 | 0 | Hydrophobic |
| F32 | CE3 | TRP- 528 | 3.96 | 0 | Hydrophobic |
| C3 | CB | TRP- 528 | 3.74 | 0 | Hydrophobic |
