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
2005-05-06
| Name: | Genome polyprotein |
|---|---|
| ID: | POLG_HCVBK |
| AC: | P26663 |
| Organism: | Hepatitis C virus genotype 1b |
| Reign: | Viruses |
| TaxID: | 11105 |
| EC Number: | 2.7.7.48 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 44.670 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.319 | 307.125 |
| % Hydrophobic | % Polar |
|---|---|
| 70.33 | 29.67 |
| According to VolSite | |
| HET Code: | POO |
|---|---|
| Formula: | C31H39N3O3 |
| Molecular weight: | 501.660 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 43.96 % |
| Polar Surface area: | 69.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 28.8814 | 11.4398 | 5.639 |
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 | CG1 | VAL- 37 | 3.45 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 392 | 3.64 | 0 | Hydrophobic |
| C12 | CB | LEU- 392 | 4.17 | 0 | Hydrophobic |
| C13 | CB | ALA- 393 | 4.38 | 0 | Hydrophobic |
| C20 | CB | ALA- 395 | 3.89 | 0 | Hydrophobic |
| C16 | CB | ALA- 396 | 4.18 | 0 | Hydrophobic |
| C15 | CB | ALA- 396 | 3.68 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 424 | 3.6 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 425 | 3.91 | 0 | Hydrophobic |
| C21 | CB | HIS- 428 | 3.79 | 0 | Hydrophobic |
| C21 | CE1 | PHE- 429 | 3.83 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 492 | 4.24 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 492 | 3.72 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 494 | 4.25 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 494 | 3.85 | 0 | Hydrophobic |
| C1 | CB | VAL- 494 | 3.96 | 0 | Hydrophobic |
| C5 | CG | PRO- 495 | 3.95 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 503 | 2.83 | 135 | H-Bond (Protein Donor) |
| O1 | NH1 | ARG- 503 | 2.57 | 149.12 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 503 | 3.11 | 0 | Ionic (Protein Cationic) |
