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
2011-01-24
| Name: | Genome polyprotein |
|---|---|
| ID: | POLG_HCVCO |
| AC: | Q9WMX2 |
| Organism: | Hepatitis C virus genotype 1b |
| Reign: | Viruses |
| TaxID: | 333284 |
| EC Number: | 2.7.7.48 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 44.386 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.950 | 263.250 |
| % Hydrophobic | % Polar |
|---|---|
| 69.23 | 30.77 |
| According to VolSite | |
| HET Code: | 23E |
|---|---|
| Formula: | C38H37N4O5 |
| Molecular weight: | 629.724 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 42.37 % |
| Polar Surface area: | 132.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 7 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 13.9084 | 2.56572 | 100.158 |
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 |
| C34 | CD2 | LEU- 392 | 3.72 | 0 | Hydrophobic |
| C40 | CB | LEU- 392 | 4.26 | 0 | Hydrophobic |
| C41 | CB | ALA- 393 | 4.42 | 0 | Hydrophobic |
| C35 | CB | ALA- 395 | 3.5 | 0 | Hydrophobic |
| C36 | CB | ALA- 396 | 4.36 | 0 | Hydrophobic |
| C41 | CB | ALA- 396 | 3.57 | 0 | Hydrophobic |
| C36 | CG2 | THR- 399 | 4.12 | 0 | Hydrophobic |
| C34 | CG2 | ILE- 424 | 3.61 | 0 | Hydrophobic |
| C35 | CD2 | LEU- 425 | 4.02 | 0 | Hydrophobic |
| C35 | CB | HIS- 428 | 4.33 | 0 | Hydrophobic |
| C35 | CE2 | PHE- 429 | 3.85 | 0 | Hydrophobic |
| C39 | CB | LEU- 492 | 4.19 | 0 | Hydrophobic |
| C40 | CD1 | LEU- 492 | 3.77 | 0 | Hydrophobic |
| C41 | CD2 | LEU- 492 | 4.32 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 494 | 4.27 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 494 | 4.24 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 494 | 4.08 | 0 | Hydrophobic |
| C44 | CG2 | VAL- 494 | 3.96 | 0 | Hydrophobic |
| C39 | CG2 | VAL- 494 | 3.51 | 0 | Hydrophobic |
| C7 | CB | PRO- 495 | 3.59 | 0 | Hydrophobic |
| C22 | CG | PRO- 495 | 3.88 | 0 | Hydrophobic |
| O15 | CZ | ARG- 498 | 3.81 | 0 | Ionic (Protein Cationic) |
| O15 | NH1 | ARG- 498 | 3.31 | 143.03 | H-Bond (Protein Donor) |
| O15 | NE | ARG- 498 | 3.47 | 139.97 | H-Bond (Protein Donor) |
| C7 | CG1 | VAL- 499 | 4.3 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 499 | 3.61 | 0 | Hydrophobic |
| O38 | NH1 | ARG- 503 | 2.8 | 143.45 | H-Bond (Protein Donor) |
| O38 | NH2 | ARG- 503 | 2.8 | 143.47 | H-Bond (Protein Donor) |
