sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.140 Å
X-ray
2012-08-16
| Name: | Genome polyprotein |
|---|---|
| ID: | POLG_HCVBK |
| AC: | P26663 |
| Organism: | Hepatitis C virus genotype 1b |
| Reign: | Viruses |
| TaxID: | 11105 |
| EC Number: | 3.4.21.98 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.688 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.541 | 577.125 |
| % Hydrophobic | % Polar |
|---|---|
| 33.33 | 66.67 |
| According to VolSite | |
| HET Code: | PW1 |
|---|---|
| Formula: | C13H12F2NO |
| Molecular weight: | 236.237 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.59 % |
| Polar Surface area: | 36.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 4.46924 | 14.9125 | -40.7422 |
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 |
| F | CD2 | TYR- 56 | 3.83 | 0 | Hydrophobic |
| F | CB | HIS- 57 | 3.52 | 0 | Hydrophobic |
| C12 | CB | HIS- 57 | 4.07 | 0 | Hydrophobic |
| C4 | CB | ASP- 81 | 3.88 | 0 | Hydrophobic |
| C5 | CB | ASP- 81 | 3.52 | 0 | Hydrophobic |
| F | SD | MET- 485 | 3.6 | 0 | Hydrophobic |
| C10 | CG | MET- 485 | 4 | 0 | Hydrophobic |
| C11 | SD | MET- 485 | 4.27 | 0 | Hydrophobic |
| C9 | CB | MET- 485 | 3.83 | 0 | Hydrophobic |
| C7 | CB | VAL- 524 | 4.28 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 524 | 4.48 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 524 | 3.53 | 0 | Hydrophobic |
| F2 | CG | GLN- 526 | 3.52 | 0 | Hydrophobic |
| C11 | CG | GLN- 526 | 4.18 | 0 | Hydrophobic |
| N3 | OE2 | GLU- 628 | 3.44 | 156.83 | H-Bond (Ligand Donor) |
| N3 | OE2 | GLU- 628 | 3.44 | 0 | Ionic (Ligand Cationic) |
| C11 | CG1 | VAL- 630 | 4.22 | 0 | Hydrophobic |
| F2 | CG1 | VAL- 630 | 4.47 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 630 | 3.8 | 0 | Hydrophobic |
