sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.820 Å
X-ray
2007-11-12
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B5 |
| AC: | P04587 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11682 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.457 |
|---|---|
| Number of residues: | 16 |
| Including | |
| Standard Amino Acids: | 15 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.316 | 286.875 |
| % Hydrophobic | % Polar |
|---|---|
| 51.76 | 48.24 |
| According to VolSite | |
| HET Code: | LLG |
|---|---|
| Formula: | C14H16NO2 |
| Molecular weight: | 230.282 g/mol |
| DrugBank ID: | DB08115 |
| Buried Surface Area: | 31.5 % |
| Polar Surface area: | 53.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 9.42412 | 9.03965 | -3.45694 |
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 |
| N1 | OD1 | ASP- 25 | 2.79 | 152.96 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 25 | 2.92 | 136.85 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 25 | 2.79 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 25 | 2.92 | 0 | Ionic (Ligand Cationic) |
| C17 | CD1 | ILE- 47 | 4.34 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 54 | 4.25 | 0 | Hydrophobic |
| C17 | CB | THR- 80 | 4.33 | 0 | Hydrophobic |
| C13 | CG | PRO- 81 | 4.05 | 0 | Hydrophobic |
| C12 | CG | PRO- 81 | 3.56 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 82 | 3.34 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 82 | 3.33 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 82 | 3.65 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 84 | 3.87 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 84 | 4.44 | 0 | Hydrophobic |
