sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.760 Å
X-ray
2013-11-25
| 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: | 23.136 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.076 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 57.27 | 42.73 |
| According to VolSite | |
| HET Code: | LOZ |
|---|---|
| Formula: | C22H24N2O5 |
| Molecular weight: | 396.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.2 % |
| Polar Surface area: | 115.33 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: | 7 |
| X | Y | Z |
|---|---|---|
| 80.2842 | 33.7851 | -16.089 |
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 |
| C9 | CB | GLN- 95 | 4.26 | 0 | Hydrophobic |
| C7 | CB | ALA- 98 | 4.21 | 0 | Hydrophobic |
| C13 | CD1 | TYR- 99 | 4.11 | 0 | Hydrophobic |
| C11 | CB | TYR- 99 | 4.12 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 102 | 3.7 | 0 | Hydrophobic |
| C7 | CG2 | THR- 125 | 3.64 | 0 | Hydrophobic |
| C7 | CG2 | THR- 125 | 3.64 | 0 | Hydrophobic |
| C27 | CB | ALA- 129 | 3.68 | 0 | Hydrophobic |
| C25 | CB | TRP- 132 | 3.61 | 0 | Hydrophobic |
| N51 | OE2 | GLU- 170 | 3.77 | 0 | Ionic (Ligand Cationic) |
| O1 | N | GLU- 170 | 2.96 | 166.37 | H-Bond (Protein Donor) |
| C42 | CG | GLU- 170 | 4.32 | 0 | Hydrophobic |
| O3 | N | HIS- 171 | 3.05 | 160.99 | H-Bond (Protein Donor) |
| C13 | CG | LYS- 173 | 4.48 | 0 | Hydrophobic |
| C17 | CB | THR- 174 | 4.26 | 0 | Hydrophobic |
| C5 | CG2 | THR- 174 | 4.07 | 0 | Hydrophobic |
| C31 | CG2 | THR- 174 | 3.58 | 0 | Hydrophobic |
| O3 | OG1 | THR- 174 | 2.67 | 156.22 | H-Bond (Protein Donor) |
| C24 | CE | MET- 178 | 3.52 | 0 | Hydrophobic |
