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
2013-12-07
| 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 | 46 % |
| B | 54 % |
| B-Factor: | 20.985 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.773 | 347.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.31 | 43.69 |
| According to VolSite | |
| HET Code: | Y7N |
|---|---|
| Formula: | C24H26N2O5 |
| Molecular weight: | 422.474 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.07 % |
| 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: | 8 |
| X | Y | Z |
|---|---|---|
| -11.0682 | 45.3106 | 1.04152 |
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 |
| C11 | CG | GLN- 95 | 3.55 | 0 | Hydrophobic |
| C6 | CB | ALA- 98 | 4.24 | 0 | Hydrophobic |
| C18 | CD1 | TYR- 99 | 4.1 | 0 | Hydrophobic |
| C11 | CB | TYR- 99 | 4.08 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 102 | 3.69 | 0 | Hydrophobic |
| C4 | CG2 | THR- 125 | 3.75 | 0 | Hydrophobic |
| C2 | CB | ALA- 129 | 3.82 | 0 | Hydrophobic |
| C5 | CB | TRP- 132 | 3.76 | 0 | Hydrophobic |
| N25 | O | ASP- 167 | 2.77 | 157.92 | H-Bond (Ligand Donor) |
| N26 | O | GLN- 168 | 2.73 | 145.71 | H-Bond (Ligand Donor) |
| O31 | N | GLU- 170 | 2.89 | 160.17 | H-Bond (Protein Donor) |
| C21 | CB | GLU- 170 | 4.37 | 0 | Hydrophobic |
| O27 | N | HIS- 171 | 2.97 | 161.64 | H-Bond (Protein Donor) |
| C12 | CB | THR- 174 | 4.27 | 0 | Hydrophobic |
| C3 | CG2 | THR- 174 | 3.73 | 0 | Hydrophobic |
| C9 | CG2 | THR- 174 | 4.06 | 0 | Hydrophobic |
| O27 | OG1 | THR- 174 | 2.6 | 159.33 | H-Bond (Protein Donor) |
| C5 | CE | MET- 178 | 3.4 | 0 | Hydrophobic |
| C10 | CE | MET- 178 | 3.67 | 0 | Hydrophobic |
