sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2013-11-14
| 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 | 42 % |
| B | 58 % |
| B-Factor: | 21.663 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.817 | 361.125 |
| % Hydrophobic | % Polar |
|---|---|
| 52.34 | 47.66 |
| According to VolSite | |
| HET Code: | 7NV |
|---|---|
| Formula: | C23H26N3O6 |
| Molecular weight: | 440.469 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 48.26 % |
| Polar Surface area: | 120.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 11.1717 | -46.6499 | 1.14806 |
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 |
| C25 | CB | GLN- 95 | 4.32 | 0 | Hydrophobic |
| C3 | CG | GLN- 95 | 3.36 | 0 | Hydrophobic |
| C24 | CB | ALA- 98 | 3.9 | 0 | Hydrophobic |
| C24 | CB | TYR- 99 | 4.13 | 0 | Hydrophobic |
| C23 | CG2 | THR- 125 | 3.86 | 0 | Hydrophobic |
| C19 | CG2 | THR- 125 | 3.78 | 0 | Hydrophobic |
| C7 | CB | GLU- 170 | 4.41 | 0 | Hydrophobic |
| C5 | CB | GLU- 170 | 4.1 | 0 | Hydrophobic |
| C17 | CB | GLU- 170 | 3.84 | 0 | Hydrophobic |
| O33 | N | GLU- 170 | 2.99 | 162.09 | H-Bond (Protein Donor) |
| O32 | N | HIS- 171 | 3 | 153.2 | H-Bond (Protein Donor) |
| O32 | OG1 | THR- 174 | 2.79 | 156.97 | H-Bond (Protein Donor) |
| C22 | CG2 | THR- 174 | 3.67 | 0 | Hydrophobic |
