sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2009-04-30
| 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: | 20.299 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.052 | 438.750 |
| % Hydrophobic | % Polar |
|---|---|
| 29.23 | 70.77 |
| According to VolSite | |
| HET Code: | B5P |
|---|---|
| Formula: | C19H21N6O6S2 |
| Molecular weight: | 493.537 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.95 % |
| Polar Surface area: | 182.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -33.3692 | 8.45897 | -8.57576 |
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 |
| C3 | CG | PRO- 197 | 3.87 | 0 | Hydrophobic |
| C3 | CD | ARG- 200 | 4.17 | 0 | Hydrophobic |
| C18 | CG2 | THR- 287 | 4.39 | 0 | Hydrophobic |
| O6 | ND2 | ASN- 291 | 2.8 | 173.96 | H-Bond (Protein Donor) |
| C15 | CB | ASN- 316 | 4.2 | 0 | Hydrophobic |
| O6 | N | ASP- 318 | 3.21 | 138.13 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 318 | 2.94 | 176.04 | H-Bond (Ligand Donor) |
| C16 | CB | ASP- 319 | 4.21 | 0 | Hydrophobic |
| C15 | SG | CYS- 366 | 4.14 | 0 | Hydrophobic |
| C4 | CB | CYS- 366 | 4.05 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 384 | 4.2 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 384 | 3.52 | 0 | Hydrophobic |
| C2 | CE | MET- 414 | 3.56 | 0 | Hydrophobic |
| C1 | CZ | TYR- 415 | 3.63 | 0 | Hydrophobic |
| C5 | CZ | TYR- 415 | 4.1 | 0 | Hydrophobic |
| C2 | CE1 | TYR- 448 | 4.45 | 0 | Hydrophobic |
| C3 | CZ | TYR- 448 | 4.33 | 0 | Hydrophobic |
| O2 | N | TYR- 448 | 2.99 | 140.97 | H-Bond (Protein Donor) |
| C18 | CB | SER- 556 | 3.97 | 0 | Hydrophobic |
| C19 | CB | SER- 556 | 3.96 | 0 | Hydrophobic |
