sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.390 Å
X-ray
2009-03-18
| 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: | 28.069 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.969 | 907.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.15 | 59.85 |
| According to VolSite | |
| HET Code: | XNC |
|---|---|
| Formula: | C34H32FN3O5S |
| Molecular weight: | 613.698 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.57 % |
| Polar Surface area: | 117.21 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 27.5759 | 54.6412 | 10.7544 |
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 |
| F34 | CE1 | PHE- 193 | 3.25 | 0 | Hydrophobic |
| C29 | CG | PRO- 197 | 3.86 | 0 | Hydrophobic |
| C26 | CD | ARG- 200 | 3.89 | 0 | Hydrophobic |
| C27 | CD | ARG- 200 | 3.25 | 0 | Hydrophobic |
| C23 | SG | CYS- 366 | 4.4 | 0 | Hydrophobic |
| C25 | CB | CYS- 366 | 3.67 | 0 | Hydrophobic |
| C2 | CB | CYS- 366 | 3.62 | 0 | Hydrophobic |
| C21 | CB | CYS- 366 | 3.3 | 0 | Hydrophobic |
| O36 | OG | SER- 367 | 2.71 | 166.7 | H-Bond (Ligand Donor) |
| C6 | CB | SER- 367 | 4.46 | 0 | Hydrophobic |
| C31 | CB | SER- 368 | 3.69 | 0 | Hydrophobic |
| C30 | CB | LEU- 384 | 3.94 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 384 | 3.95 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 384 | 4 | 0 | Hydrophobic |
| C37 | CB | SER- 407 | 4.36 | 0 | Hydrophobic |
| C38 | CG | MET- 414 | 3.91 | 0 | Hydrophobic |
| C30 | CB | MET- 414 | 4.26 | 0 | Hydrophobic |
| C20 | CE | MET- 414 | 4.27 | 0 | Hydrophobic |
| C27 | CE | MET- 414 | 3.66 | 0 | Hydrophobic |
| C28 | CE | MET- 414 | 3.25 | 0 | Hydrophobic |
| C13 | CB | GLN- 446 | 4.18 | 0 | Hydrophobic |
| O32 | N | TYR- 448 | 3 | 151.87 | H-Bond (Protein Donor) |
| F34 | CD1 | TYR- 448 | 3.68 | 0 | Hydrophobic |
| O33 | N | GLY- 449 | 2.91 | 161.55 | H-Bond (Protein Donor) |
| C44 | CB | SER- 556 | 4.05 | 0 | Hydrophobic |
| N39 | OG | SER- 556 | 3.06 | 148.3 | H-Bond (Protein Donor) |
