sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2013-12-23
| 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 | 58 % |
| B | 42 % |
| B-Factor: | 18.295 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.044 | 361.125 |
| % Hydrophobic | % Polar |
|---|---|
| 59.81 | 40.19 |
| According to VolSite | |
| HET Code: | OM1 |
|---|---|
| Formula: | C25H24N2O6 |
| Molecular weight: | 448.468 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.36 % |
| Polar Surface area: | 113.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -9.37406 | 7.03179 | -14.5118 |
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 | CG | GLN- 95 | 3.79 | 0 | Hydrophobic |
| C24 | CB | ALA- 98 | 4.4 | 0 | Hydrophobic |
| C12 | CB | ALA- 98 | 4.03 | 0 | Hydrophobic |
| C25 | CB | TYR- 99 | 4.32 | 0 | Hydrophobic |
| C27 | CD1 | TYR- 99 | 3.94 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 102 | 3.88 | 0 | Hydrophobic |
| C9 | CG2 | THR- 125 | 4.18 | 0 | Hydrophobic |
| C23 | CG2 | THR- 125 | 4.04 | 0 | Hydrophobic |
| C10 | CB | ALA- 128 | 3.59 | 0 | Hydrophobic |
| C12 | CB | ALA- 129 | 3.96 | 0 | Hydrophobic |
| C8 | CB | ALA- 129 | 3.99 | 0 | Hydrophobic |
| N3 | O | GLN- 168 | 2.81 | 160.58 | H-Bond (Ligand Donor) |
| O32 | N | GLU- 170 | 2.86 | 162.3 | H-Bond (Protein Donor) |
| C17 | CB | GLU- 170 | 4.42 | 0 | Hydrophobic |
| O33 | N | HIS- 171 | 2.9 | 163.12 | H-Bond (Protein Donor) |
| C7 | CG2 | THR- 174 | 4.41 | 0 | Hydrophobic |
| C12 | CG2 | THR- 174 | 4.3 | 0 | Hydrophobic |
| C30 | CG2 | THR- 174 | 4.05 | 0 | Hydrophobic |
| O33 | OG1 | THR- 174 | 2.76 | 166.58 | H-Bond (Protein Donor) |
| C6 | CE | MET- 178 | 3.48 | 0 | Hydrophobic |
