sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 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 | 48 % |
| B | 52 % |
| B-Factor: | 23.864 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.975 | 421.875 |
| % Hydrophobic | % Polar |
|---|---|
| 48.00 | 52.00 |
| According to VolSite | |
| HET Code: | WOP |
|---|---|
| Formula: | C26H24N3O6 |
| Molecular weight: | 474.485 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.39 % |
| Polar Surface area: | 120.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 11.0334 | -46.9982 | 1.76294 |
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 |
| C22 | CB | GLN- 95 | 4.35 | 0 | Hydrophobic |
| C5 | CG | GLN- 95 | 3.66 | 0 | Hydrophobic |
| C17 | CB | GLN- 95 | 4.26 | 0 | Hydrophobic |
| C12 | CB | ALA- 98 | 3.76 | 0 | Hydrophobic |
| C12 | CB | TYR- 99 | 4.36 | 0 | Hydrophobic |
| C9 | CG2 | THR- 125 | 3.8 | 0 | Hydrophobic |
| C12 | CG2 | THR- 125 | 3.66 | 0 | Hydrophobic |
| N27 | O | GLN- 168 | 3.32 | 130.37 | H-Bond (Ligand Donor) |
| O31 | N | GLU- 170 | 2.92 | 164.66 | H-Bond (Protein Donor) |
| C10 | CB | GLU- 170 | 3.76 | 0 | Hydrophobic |
| C3 | CB | GLU- 170 | 3.85 | 0 | Hydrophobic |
| O30 | N | HIS- 171 | 3 | 162.47 | H-Bond (Protein Donor) |
| O35 | ND1 | HIS- 171 | 2.99 | 157.18 | H-Bond (Protein Donor) |
| O30 | OG1 | THR- 174 | 2.76 | 154.94 | H-Bond (Protein Donor) |
| C16 | CG2 | THR- 174 | 3.78 | 0 | Hydrophobic |
