sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2011-09-26
| 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: | 23.884 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.408 | 2146.500 |
| % Hydrophobic | % Polar |
|---|---|
| 38.84 | 61.16 |
| According to VolSite | |
| HET Code: | HI3 |
|---|---|
| Formula: | C25H20F3N3O4S |
| Molecular weight: | 515.504 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.62 % |
| Polar Surface area: | 105.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 23.2199 | 0.737722 | 2.15644 |
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 |
| F2 | CZ | PHE- 193 | 3.5 | 0 | Hydrophobic |
| C25 | CE1 | PHE- 193 | 4.13 | 0 | Hydrophobic |
| C24 | CB | PRO- 197 | 4.49 | 0 | Hydrophobic |
| C13 | CD | ARG- 200 | 4.27 | 0 | Hydrophobic |
| C12 | CB | ASN- 316 | 4.14 | 0 | Hydrophobic |
| C2 | CB | ASP- 319 | 3.89 | 0 | Hydrophobic |
| F2 | CB | ASP- 319 | 4.46 | 0 | Hydrophobic |
| C4 | CB | CYS- 366 | 3.59 | 0 | Hydrophobic |
| C5 | CB | CYS- 366 | 3.57 | 0 | Hydrophobic |
| C9 | SG | CYS- 366 | 3.47 | 0 | Hydrophobic |
| F1 | CB | SER- 367 | 3.24 | 0 | Hydrophobic |
| F3 | CB | SER- 368 | 4.47 | 0 | Hydrophobic |
| F3 | CD1 | LEU- 384 | 3.5 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 384 | 4.04 | 0 | Hydrophobic |
| C3 | CE | MET- 414 | 3.7 | 0 | Hydrophobic |
| C24 | CE1 | TYR- 415 | 3.56 | 0 | Hydrophobic |
| N2 | O | GLN- 446 | 2.84 | 172.67 | H-Bond (Ligand Donor) |
| O1 | N | TYR- 448 | 2.77 | 165 | H-Bond (Protein Donor) |
| C25 | CE1 | TYR- 448 | 3.96 | 0 | Hydrophobic |
| C22 | CB | SER- 556 | 3.76 | 0 | Hydrophobic |
