sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2012-04-13
| 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: | 17.960 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.193 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 65.63 | 34.38 |
| According to VolSite | |
| HET Code: | 0S3 |
|---|---|
| Formula: | C21H29N2O3S |
| Molecular weight: | 389.532 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.37 % |
| Polar Surface area: | 91.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -8.36581 | 33.7877 | -33.121 |
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 |
| S04 | CD2 | LEU- 419 | 3.82 | 0 | Hydrophobic |
| C09 | CD2 | LEU- 419 | 4.13 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 419 | 4.47 | 0 | Hydrophobic |
| C06 | CD2 | LEU- 419 | 4.04 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 419 | 3.8 | 0 | Hydrophobic |
| C22 | CB | ARG- 422 | 3.57 | 0 | Hydrophobic |
| C10 | CE | MET- 423 | 4.07 | 0 | Hydrophobic |
| C22 | CB | MET- 423 | 4.24 | 0 | Hydrophobic |
| C17 | CB | HIS- 475 | 4.39 | 0 | Hydrophobic |
| O27 | N | SER- 476 | 2.88 | 145.74 | H-Bond (Protein Donor) |
| O26 | N | TYR- 477 | 2.76 | 150.12 | H-Bond (Protein Donor) |
| C18 | CE1 | TYR- 477 | 3.93 | 0 | Hydrophobic |
| S04 | CD1 | ILE- 482 | 3.78 | 0 | Hydrophobic |
| C07 | CG2 | ILE- 482 | 4.46 | 0 | Hydrophobic |
| C09 | CG2 | ILE- 482 | 4.47 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 482 | 4.43 | 0 | Hydrophobic |
| C09 | CG1 | VAL- 485 | 3.7 | 0 | Hydrophobic |
| C09 | CB | ALA- 486 | 4.22 | 0 | Hydrophobic |
| C11 | CB | ALA- 486 | 4.14 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 489 | 4.06 | 0 | Hydrophobic |
| C10 | CB | LEU- 497 | 4.11 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 497 | 4.44 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 497 | 4.13 | 0 | Hydrophobic |
| C22 | CD2 | TRP- 528 | 3.45 | 0 | Hydrophobic |
| C18 | CB | TRP- 528 | 4.23 | 0 | Hydrophobic |
| C19 | CE3 | TRP- 528 | 3.45 | 0 | Hydrophobic |
