sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2013-12-22
| Name: | Integrase |
|---|---|
| ID: | Q76353_9HIV1 |
| AC: | Q76353 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 54 % |
| B | 46 % |
| B-Factor: | 20.876 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.016 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 57.55 | 42.45 |
| According to VolSite | |
| HET Code: | VXO |
|---|---|
| Formula: | C25H27N2O5 |
| Molecular weight: | 435.492 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.79 % |
| Polar Surface area: | 103.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -34.6717 | 33.0168 | -15.166 |
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 | CG | GLN- 95 | 3.98 | 0 | Hydrophobic |
| C13 | CG | GLN- 95 | 3.65 | 0 | Hydrophobic |
| C6 | CB | ALA- 98 | 4.11 | 0 | Hydrophobic |
| C17 | CD1 | TYR- 99 | 4.43 | 0 | Hydrophobic |
| C6 | CB | TYR- 99 | 3.93 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 102 | 4.42 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 102 | 4.27 | 0 | Hydrophobic |
| C25 | CG2 | THR- 125 | 4.33 | 0 | Hydrophobic |
| C4 | CG2 | THR- 125 | 4.01 | 0 | Hydrophobic |
| C18 | CB | ALA- 128 | 4.15 | 0 | Hydrophobic |
| C22 | CB | ALA- 128 | 4.48 | 0 | Hydrophobic |
| C18 | CB | ALA- 129 | 4.21 | 0 | Hydrophobic |
| C18 | CB | TRP- 132 | 4.34 | 0 | Hydrophobic |
| C19 | CB | TRP- 132 | 4.48 | 0 | Hydrophobic |
| O29 | N | GLU- 170 | 2.86 | 162.17 | H-Bond (Protein Donor) |
| C5 | CB | GLU- 170 | 3.84 | 0 | Hydrophobic |
| C12 | CB | GLU- 170 | 3.53 | 0 | Hydrophobic |
| O28 | N | HIS- 171 | 2.95 | 161.16 | H-Bond (Protein Donor) |
| C14 | CB | THR- 174 | 4.27 | 0 | Hydrophobic |
| C21 | CG2 | THR- 174 | 3.84 | 0 | Hydrophobic |
| C10 | CG2 | THR- 174 | 3.67 | 0 | Hydrophobic |
| O28 | OG1 | THR- 174 | 2.63 | 160.41 | H-Bond (Protein Donor) |
| C24 | CE | MET- 178 | 3.7 | 0 | Hydrophobic |
