sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2013-09-04
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 19.455 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.039 | 1393.875 |
| % Hydrophobic | % Polar |
|---|---|
| 36.80 | 63.20 |
| According to VolSite | |
| HET Code: | 28R |
|---|---|
| Formula: | C24H25N3O5S |
| Molecular weight: | 467.537 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.98 % |
| Polar Surface area: | 118.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 33.9797 | -8.45688 | 13.9365 |
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 |
| C22 | CE1 | PHE- 193 | 4.35 | 0 | Hydrophobic |
| C24 | CG | PRO- 197 | 4.11 | 0 | Hydrophobic |
| C25 | CG | PRO- 197 | 4.26 | 0 | Hydrophobic |
| C25 | CD | ARG- 200 | 3.78 | 0 | Hydrophobic |
| C26 | CD | ARG- 200 | 4.4 | 0 | Hydrophobic |
| O18 | ND2 | ASN- 291 | 3.05 | 173.62 | H-Bond (Protein Donor) |
| C12 | CB | ASN- 316 | 4.34 | 0 | Hydrophobic |
| C22 | CB | ASN- 316 | 4.34 | 0 | Hydrophobic |
| N16 | OD1 | ASP- 318 | 2.89 | 153.77 | H-Bond (Ligand Donor) |
| C12 | CB | ASP- 319 | 3.63 | 0 | Hydrophobic |
| C4 | CB | CYS- 366 | 4.1 | 0 | Hydrophobic |
| C12 | SG | CYS- 366 | 3.64 | 0 | Hydrophobic |
| C22 | SG | CYS- 366 | 3.63 | 0 | Hydrophobic |
| C26 | CB | CYS- 366 | 3.99 | 0 | Hydrophobic |
| C26 | CB | SER- 368 | 3.82 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 384 | 3.95 | 0 | Hydrophobic |
| C24 | CE | MET- 414 | 4.37 | 0 | Hydrophobic |
| C25 | CE | MET- 414 | 4.43 | 0 | Hydrophobic |
| C2 | CE | MET- 414 | 3.63 | 0 | Hydrophobic |
| C24 | CZ | TYR- 415 | 3.77 | 0 | Hydrophobic |
| N30 | O | GLN- 446 | 2.72 | 169.35 | H-Bond (Ligand Donor) |
| C22 | CE1 | TYR- 448 | 3.68 | 0 | Hydrophobic |
| C25 | CE1 | TYR- 448 | 4.23 | 0 | Hydrophobic |
| O29 | N | TYR- 448 | 2.82 | 160.64 | H-Bond (Protein Donor) |
| C20 | CB | SER- 556 | 3.48 | 0 | Hydrophobic |
