sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.290 Å
X-ray
2010-12-16
| 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: | 38.502 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.095 | 290.250 |
| % Hydrophobic | % Polar |
|---|---|
| 70.93 | 29.07 |
| According to VolSite | |
| HET Code: | 23E |
|---|---|
| Formula: | C38H37N4O5 |
| Molecular weight: | 629.724 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 41.95 % |
| 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 |
|---|---|---|
| 14.0763 | 2.21438 | 99.5749 |
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 | 3.69 | 0 | Hydrophobic |
| C40 | CB | LEU- 392 | 4.28 | 0 | Hydrophobic |
| C41 | CB | ALA- 393 | 4.42 | 0 | Hydrophobic |
| C35 | CB | ALA- 395 | 3.64 | 0 | Hydrophobic |
| C37 | CB | ALA- 396 | 4.22 | 0 | Hydrophobic |
| C40 | CB | ALA- 396 | 3.66 | 0 | Hydrophobic |
| C36 | CB | THR- 399 | 4.47 | 0 | Hydrophobic |
| C34 | CG2 | ILE- 424 | 3.58 | 0 | Hydrophobic |
| C34 | CD2 | LEU- 425 | 4.1 | 0 | Hydrophobic |
| C35 | CB | HIS- 428 | 4.22 | 0 | Hydrophobic |
| C35 | CE2 | PHE- 429 | 3.88 | 0 | Hydrophobic |
| C39 | CB | LEU- 492 | 4.28 | 0 | Hydrophobic |
| C40 | CD1 | LEU- 492 | 3.84 | 0 | Hydrophobic |
| C41 | CD2 | LEU- 492 | 4.09 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 494 | 4.22 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 494 | 4.11 | 0 | Hydrophobic |
| C44 | CG2 | VAL- 494 | 4 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 494 | 4.22 | 0 | Hydrophobic |
| C39 | CG2 | VAL- 494 | 3.55 | 0 | Hydrophobic |
| C22 | CG | PRO- 495 | 4.1 | 0 | Hydrophobic |
| C7 | CB | PRO- 495 | 3.6 | 0 | Hydrophobic |
| O15 | NE | ARG- 498 | 3.13 | 135.93 | H-Bond (Protein Donor) |
| O15 | NH1 | ARG- 498 | 3.08 | 134.54 | H-Bond (Protein Donor) |
| O20 | NH1 | ARG- 498 | 3.21 | 133.34 | H-Bond (Protein Donor) |
| O15 | CZ | ARG- 498 | 3.49 | 0 | Ionic (Protein Cationic) |
| C8 | CG2 | VAL- 499 | 3.78 | 0 | Hydrophobic |
| O6 | NH2 | ARG- 503 | 3.1 | 121.82 | H-Bond (Protein Donor) |
| O38 | NH1 | ARG- 503 | 2.72 | 146.74 | H-Bond (Protein Donor) |
| O38 | NH2 | ARG- 503 | 2.83 | 140.69 | H-Bond (Protein Donor) |
