sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2010-06-10
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1N5 |
| AC: | P12497 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11698 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.548 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.267 | 631.125 |
| % Hydrophobic | % Polar |
|---|---|
| 56.68 | 43.32 |
| According to VolSite | |
| HET Code: | CBJ |
|---|---|
| Formula: | C18H11BrNO6 |
| Molecular weight: | 417.187 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.19 % |
| Polar Surface area: | 95.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 10.2032 | -25.5576 | -10.1973 |
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 |
| C15 | CG1 | VAL- 77 | 4.11 | 0 | Hydrophobic |
| BR8 | CD1 | ILE- 84 | 4.36 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 84 | 3.63 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 150 | 4.08 | 0 | Hydrophobic |
| C10 | SD | MET- 154 | 3.28 | 0 | Hydrophobic |
| C7 | CG | MET- 154 | 3.32 | 0 | Hydrophobic |
| C6 | CB | GLU- 157 | 3.87 | 0 | Hydrophobic |
| BR8 | CB | GLU- 157 | 4.38 | 0 | Hydrophobic |
| C7 | CG | LEU- 158 | 4.35 | 0 | Hydrophobic |
| BR8 | CD2 | LEU- 158 | 3.42 | 0 | Hydrophobic |
| BR8 | CD1 | ILE- 161 | 4.16 | 0 | Hydrophobic |
| BR8 | CB | HIS- 183 | 3.82 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 183 | 3.59 | 0 | Aromatic Face/Face |
| O25 | NZ | LYS- 188 | 3.97 | 0 | Ionic (Protein Cationic) |
