sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2011-07-01
| 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 | 44 % |
| B | 56 % |
| B-Factor: | 19.626 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.725 | 344.250 |
| % Hydrophobic | % Polar |
|---|---|
| 52.94 | 47.06 |
| According to VolSite | |
| HET Code: | OM3 |
|---|---|
| Formula: | C25H30N2O5 |
| Molecular weight: | 438.516 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 48.57 % |
| Polar Surface area: | 92.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -11.1585 | 45.7461 | 1.25622 |
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 |
| C6 | CB | GLN- 95 | 3.76 | 0 | Hydrophobic |
| C11 | CB | TYR- 99 | 4.22 | 0 | Hydrophobic |
| C20 | CD1 | TYR- 99 | 3.89 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 102 | 4.37 | 0 | Hydrophobic |
| C5 | CG2 | THR- 125 | 3.87 | 0 | Hydrophobic |
| C19 | CB | ALA- 128 | 4.22 | 0 | Hydrophobic |
| C15 | CB | ALA- 129 | 3.89 | 0 | Hydrophobic |
| C17 | CB | TRP- 132 | 3.69 | 0 | Hydrophobic |
| N26 | O | GLN- 168 | 2.67 | 172.93 | H-Bond (Ligand Donor) |
| O30 | N | GLU- 170 | 2.68 | 165.5 | H-Bond (Protein Donor) |
| C4 | CB | GLU- 170 | 4.23 | 0 | Hydrophobic |
| O28 | N | HIS- 171 | 2.81 | 164.25 | H-Bond (Protein Donor) |
| C16 | CG2 | THR- 174 | 3.78 | 0 | Hydrophobic |
| C8 | CG2 | THR- 174 | 4.14 | 0 | Hydrophobic |
| O28 | OG1 | THR- 174 | 2.74 | 170.67 | H-Bond (Protein Donor) |
| C17 | CE | MET- 178 | 3.6 | 0 | Hydrophobic |
