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
2013-12-04
| 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 | 71 % |
| B | 29 % |
| B-Factor: | 21.858 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.692 | 405.000 |
| % Hydrophobic | % Polar |
|---|---|
| 49.17 | 50.83 |
| According to VolSite | |
| HET Code: | C5Q |
|---|---|
| Formula: | C17H12NO4 |
| Molecular weight: | 294.281 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.4 % |
| Polar Surface area: | 74.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -8.25664 | 43.7721 | 13.4319 |
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 | CB | ALA- 98 | 4.22 | 0 | Hydrophobic |
| C11 | CB | ALA- 98 | 3.83 | 0 | Hydrophobic |
| C12 | CB | ALA- 98 | 3.85 | 0 | Hydrophobic |
| C17 | CB | TYR- 99 | 4.12 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 102 | 3.71 | 0 | Hydrophobic |
| C12 | CG2 | THR- 125 | 4.17 | 0 | Hydrophobic |
| C3 | CB | ALA- 128 | 4.06 | 0 | Hydrophobic |
| C15 | CB | ALA- 128 | 4.11 | 0 | Hydrophobic |
| C4 | CB | ALA- 129 | 3.72 | 0 | Hydrophobic |
| C4 | CB | ALA- 129 | 3.72 | 0 | Hydrophobic |
| C1 | CZ3 | TRP- 131 | 3.43 | 0 | Hydrophobic |
| C3 | CB | TRP- 132 | 4.29 | 0 | Hydrophobic |
| C15 | CB | TRP- 132 | 4.29 | 0 | Hydrophobic |
| N18 | O | GLN- 168 | 2.85 | 168.52 | H-Bond (Ligand Donor) |
| C5 | CB | GLN- 168 | 4.12 | 0 | Hydrophobic |
| C6 | CG2 | THR- 174 | 3.91 | 0 | Hydrophobic |
| C4 | CE | MET- 178 | 4.44 | 0 | Hydrophobic |
| C10 | CE | MET- 178 | 4.38 | 0 | Hydrophobic |
