sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2013-05-20
| Name: | Genome polyprotein |
|---|---|
| ID: | POLG_HCVJA |
| AC: | P26662 |
| Organism: | Hepatitis C virus genotype 1b |
| Reign: | Viruses |
| TaxID: | 11116 |
| EC Number: | 3.4.21.98 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 71 % |
| C | 29 % |
| B-Factor: | 39.505 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.065 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 41.44 | 58.56 |
| According to VolSite | |
| HET Code: | 1X3 |
|---|---|
| Formula: | C37H51N5O9S |
| Molecular weight: | 741.894 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.41 % |
| Polar Surface area: | 188.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 7 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 50.4949 | 38.4714 | 105.704 |
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 |
| C52 | CG | GLN- 41 | 4.15 | 0 | Hydrophobic |
| C51 | CD1 | PHE- 43 | 3.87 | 0 | Hydrophobic |
| C38 | CB | ASN- 49 | 3.91 | 0 | Hydrophobic |
| C42 | CG2 | VAL- 51 | 3.55 | 0 | Hydrophobic |
| C51 | CG2 | VAL- 55 | 4.34 | 0 | Hydrophobic |
| N7 | NE2 | HIS- 57 | 3.16 | 142.59 | H-Bond (Ligand Donor) |
| C12 | CB | HIS- 57 | 4.38 | 0 | Hydrophobic |
| C42 | CE | MET- 74 | 4.32 | 0 | Hydrophobic |
| C46 | SD | MET- 74 | 4.04 | 0 | Hydrophobic |
| C24 | CE | MET- 74 | 4.33 | 0 | Hydrophobic |
| O22 | OH | TYR- 75 | 2.74 | 124.82 | H-Bond (Protein Donor) |
| C38 | CB | ASP- 81 | 3.75 | 0 | Hydrophobic |
| C46 | CB | PRO- 86 | 3.9 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 132 | 3.56 | 0 | Hydrophobic |
| C27 | CG | LYS- 136 | 3.94 | 0 | Hydrophobic |
| O5 | N | GLY- 137 | 2.72 | 149.38 | H-Bond (Protein Donor) |
| O49 | N | GLY- 137 | 3.02 | 122.73 | H-Bond (Protein Donor) |
| C1 | CB | SER- 139 | 3.91 | 0 | Hydrophobic |
| O50 | OG | SER- 139 | 2.58 | 149.73 | H-Bond (Protein Donor) |
| C1 | CE2 | PHE- 154 | 3.3 | 0 | Hydrophobic |
| C3 | CZ | PHE- 154 | 3.88 | 0 | Hydrophobic |
| N4 | O | ARG- 155 | 3.01 | 156.83 | H-Bond (Ligand Donor) |
| C35 | CD | ARG- 155 | 3.71 | 0 | Hydrophobic |
| C41 | CD | ARG- 155 | 3.75 | 0 | Hydrophobic |
| C36 | CB | ALA- 156 | 3.96 | 0 | Hydrophobic |
| C44 | CB | ALA- 156 | 3.84 | 0 | Hydrophobic |
| O19 | N | ALA- 157 | 2.76 | 145.92 | H-Bond (Protein Donor) |
| N20 | O | ALA- 157 | 3 | 158.97 | H-Bond (Ligand Donor) |
| C28 | CB | ALA- 157 | 3.78 | 0 | Hydrophobic |
| C3 | CB | ALA- 157 | 4.11 | 0 | Hydrophobic |
| C45 | CG2 | VAL- 158 | 3.77 | 0 | Hydrophobic |
| C44 | CB | ASP- 168 | 3.63 | 0 | Hydrophobic |
