sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 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 | 87 % |
| B | 13 % |
| B-Factor: | 67.362 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.866 | 320.625 |
| % Hydrophobic | % Polar |
|---|---|
| 86.32 | 13.68 |
| According to VolSite | |
| HET Code: | SBN |
|---|---|
| Formula: | C15H14N2O2S |
| Molecular weight: | 286.349 g/mol |
| DrugBank ID: | DB08528 |
| Buried Surface Area: | 76.86 % |
| Polar Surface area: | 92.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -0.5857 | -35.1748 | 24.0709 |
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 | CD2 | LEU- 100 | 3.75 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 100 | 3.98 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 100 | 4.31 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 100 | 3.71 | 0 | Hydrophobic |
| N1 | O | LYS- 101 | 3.09 | 148.19 | H-Bond (Ligand Donor) |
| C3 | CG | LYS- 103 | 4.01 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 106 | 4.01 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 106 | 3.21 | 0 | Hydrophobic |
| C15 | CG | GLU- 138 | 3.8 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 179 | 3.97 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 179 | 4.28 | 0 | Hydrophobic |
| C14 | CD1 | TYR- 181 | 3.79 | 0 | Hydrophobic |
| C10 | CD1 | TYR- 181 | 3.12 | 0 | Hydrophobic |
| C11 | CB | TYR- 181 | 3.52 | 0 | Hydrophobic |
| C14 | CD2 | TYR- 188 | 4.23 | 0 | Hydrophobic |
| C8 | CB | TYR- 188 | 3.65 | 0 | Hydrophobic |
| C14 | CE2 | TRP- 229 | 3.68 | 0 | Hydrophobic |
| C1 | CG | LEU- 234 | 4.48 | 0 | Hydrophobic |
| C6 | CB | LEU- 234 | 3.96 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 234 | 4.49 | 0 | Hydrophobic |
