sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2009-07-27
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1H2 |
| AC: | P04585 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11706 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 52.078 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.393 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 69.50 | 30.50 |
| According to VolSite | |
| HET Code: | ZZE |
|---|---|
| Formula: | C17H18N4O2 |
| Molecular weight: | 310.350 g/mol |
| DrugBank ID: | DB11649 |
| Buried Surface Area: | 74.48 % |
| Polar Surface area: | 94.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 8.9687 | 12.6937 | 17.988 |
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 |
| C10 | CB | LEU- 100 | 3.95 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 100 | 3.6 | 0 | Hydrophobic |
| O18 | N | LYS- 103 | 3.28 | 163.54 | H-Bond (Protein Donor) |
| C9 | CG1 | VAL- 106 | 4.46 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 106 | 3.76 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 106 | 3.54 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 108 | 3.7 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 179 | 3.52 | 0 | Hydrophobic |
| C8 | CD2 | TYR- 181 | 4.15 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 181 | 3.84 | 0 | Hydrophobic |
| C8 | CB | TYR- 188 | 3.92 | 0 | Hydrophobic |
| C14 | CB | TYR- 188 | 4.16 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 188 | 3.79 | 0 | Aromatic Face/Face |
| C13 | CB | PHE- 227 | 4.36 | 0 | Hydrophobic |
| C19 | CB | TRP- 229 | 3.92 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 234 | 3.57 | 0 | Hydrophobic |
| O18 | O | PRO- 236 | 2.7 | 150.97 | H-Bond (Ligand Donor) |
| C10 | CZ | TYR- 318 | 3.81 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 318 | 3.95 | 0 | Hydrophobic |
