sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2001-07-16
| 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: | 53.759 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.621 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 68.31 | 31.69 |
| According to VolSite | |
| HET Code: | TNK |
|---|---|
| Formula: | C22H24N2O3 |
| Molecular weight: | 364.438 g/mol |
| DrugBank ID: | DB08634 |
| Buried Surface Area: | 75.76 % |
| Polar Surface area: | 58.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -3.08015 | -35.2837 | 24.8596 |
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 |
| C17 | CD1 | LEU- 100 | 3.99 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 100 | 3.93 | 0 | Hydrophobic |
| N10 | O | LYS- 101 | 2.7 | 175.75 | H-Bond (Ligand Donor) |
| C13 | CG1 | VAL- 106 | 3.8 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 106 | 3.89 | 0 | Hydrophobic |
| C22 | CB | VAL- 106 | 4.39 | 0 | Hydrophobic |
| C24 | CB | VAL- 106 | 4.5 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 106 | 3.46 | 0 | Hydrophobic |
| C16 | CB | CYS- 181 | 3.23 | 0 | Hydrophobic |
| C1 | CB | TYR- 188 | 4.04 | 0 | Hydrophobic |
| C15 | CB | TYR- 188 | 3.79 | 0 | Hydrophobic |
| C24 | CB | PRO- 225 | 3.89 | 0 | Hydrophobic |
| C18 | CD2 | PHE- 227 | 3.8 | 0 | Hydrophobic |
| C3 | CB | PHE- 227 | 4.29 | 0 | Hydrophobic |
| C4 | CB | TRP- 229 | 4.02 | 0 | Hydrophobic |
| C2 | CG | LEU- 234 | 4.3 | 0 | Hydrophobic |
| C17 | CB | LEU- 234 | 4.05 | 0 | Hydrophobic |
| C18 | CB | LEU- 234 | 3.89 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 234 | 3.78 | 0 | Hydrophobic |
| C22 | CB | PRO- 236 | 3.61 | 0 | Hydrophobic |
| C17 | CZ | TYR- 318 | 4.49 | 0 | Hydrophobic |
