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
2007-01-30
| 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 | 96 % |
| B | 4 % |
| B-Factor: | 56.324 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.435 | 631.125 |
| % Hydrophobic | % Polar |
|---|---|
| 64.71 | 35.29 |
| According to VolSite | |
| HET Code: | HBQ |
|---|---|
| Formula: | C14H17FN2O3 |
| Molecular weight: | 280.295 g/mol |
| DrugBank ID: | DB07884 |
| Buried Surface Area: | 71.1 % |
| Polar Surface area: | 58.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -0.902 | -35.0844 | 24.268 |
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 |
| C14 | CG | PRO- 95 | 3.62 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 100 | 4.19 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 100 | 4.17 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 100 | 4.24 | 0 | Hydrophobic |
| N2 | O | LYS- 101 | 2.82 | 150.26 | H-Bond (Ligand Donor) |
| O1 | N | LYS- 101 | 3.46 | 163.41 | H-Bond (Protein Donor) |
| C9 | CG | LYS- 103 | 4.49 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 106 | 4.43 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 106 | 3.97 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 106 | 3.73 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 179 | 3.66 | 0 | Hydrophobic |
| C12 | CD1 | TYR- 181 | 3.74 | 0 | Hydrophobic |
| C14 | CE1 | TYR- 181 | 3.92 | 0 | Hydrophobic |
| C8 | SG | CYS- 188 | 3.96 | 0 | Hydrophobic |
| C10 | SG | CYS- 188 | 4.33 | 0 | Hydrophobic |
| C13 | SG | CYS- 188 | 4.18 | 0 | Hydrophobic |
| F1 | CD2 | PHE- 227 | 3.38 | 0 | Hydrophobic |
| C13 | CD2 | TRP- 229 | 4 | 0 | Hydrophobic |
| C14 | CH2 | TRP- 229 | 3.69 | 0 | Hydrophobic |
| C6 | CB | LEU- 234 | 4.41 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 234 | 4.02 | 0 | Hydrophobic |
| F1 | CD1 | LEU- 234 | 3.42 | 0 | Hydrophobic |
