sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 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: | 67.480 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.014 | 462.375 |
| % Hydrophobic | % Polar |
|---|---|
| 63.50 | 36.50 |
| According to VolSite | |
| HET Code: | 1NZ |
|---|---|
| Formula: | C28H14F6N4O3 |
| Molecular weight: | 568.426 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.52 % |
| Polar Surface area: | 80.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -24.2399 | -21.7795 | -18.0879 |
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 |
| C13 | CD2 | LEU- 419 | 4.01 | 0 | Hydrophobic |
| F29 | CD2 | LEU- 419 | 3.21 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 419 | 4.06 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 419 | 4.01 | 0 | Hydrophobic |
| C2 | CD | ARG- 422 | 4.43 | 0 | Hydrophobic |
| C3 | CB | ARG- 422 | 4.25 | 0 | Hydrophobic |
| F28 | CG | ARG- 422 | 4.29 | 0 | Hydrophobic |
| F19 | SD | MET- 423 | 3.69 | 0 | Hydrophobic |
| F28 | CB | MET- 423 | 3.34 | 0 | Hydrophobic |
| N8 | N | SER- 476 | 2.91 | 143.43 | H-Bond (Protein Donor) |
| O18 | N | TYR- 477 | 2.88 | 153.41 | H-Bond (Protein Donor) |
| F31 | CE1 | TYR- 477 | 3.67 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 482 | 4.1 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 482 | 4.47 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 482 | 3.83 | 0 | Hydrophobic |
| F29 | CG2 | ILE- 482 | 3.56 | 0 | Hydrophobic |
| F30 | CG1 | VAL- 485 | 3.58 | 0 | Hydrophobic |
| F30 | CB | ALA- 486 | 3.74 | 0 | Hydrophobic |
| F30 | CD1 | LEU- 489 | 3.5 | 0 | Hydrophobic |
| C39 | CB | LEU- 489 | 3.55 | 0 | Hydrophobic |
| C39 | CB | VAL- 494 | 4.22 | 0 | Hydrophobic |
| F32 | CD1 | LEU- 497 | 3.62 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 497 | 4.01 | 0 | Hydrophobic |
| F28 | CE2 | TRP- 528 | 3.36 | 0 | Hydrophobic |
| F32 | CE3 | TRP- 528 | 3.89 | 0 | Hydrophobic |
| C4 | CE3 | TRP- 528 | 3.48 | 0 | Hydrophobic |
| C6 | CB | TRP- 528 | 4.44 | 0 | Hydrophobic |
