sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2013-12-19
| 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: | 23.178 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.805 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 47.75 | 52.25 |
| According to VolSite | |
| HET Code: | Q31 |
|---|---|
| Formula: | C20H24N3O5 |
| Molecular weight: | 386.422 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.22 % |
| Polar Surface area: | 116.37 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 34.489 | -32.0751 | -1.64861 |
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 |
| C2 | CB | ALA- 98 | 4.14 | 0 | Hydrophobic |
| C12 | CD1 | TYR- 99 | 4.5 | 0 | Hydrophobic |
| C2 | CB | TYR- 99 | 4.01 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 102 | 4.38 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 102 | 4.37 | 0 | Hydrophobic |
| C20 | CG2 | THR- 125 | 4.39 | 0 | Hydrophobic |
| C1 | CG2 | THR- 125 | 3.99 | 0 | Hydrophobic |
| C13 | CB | ALA- 128 | 4.17 | 0 | Hydrophobic |
| C17 | CB | ALA- 128 | 4.34 | 0 | Hydrophobic |
| C13 | CB | ALA- 129 | 4.44 | 0 | Hydrophobic |
| C13 | CB | TRP- 132 | 4.09 | 0 | Hydrophobic |
| C14 | CB | GLN- 168 | 4.43 | 0 | Hydrophobic |
| O25 | N | GLU- 170 | 2.96 | 161.95 | H-Bond (Protein Donor) |
| O24 | N | HIS- 171 | 2.96 | 157.82 | H-Bond (Protein Donor) |
| O28 | ND1 | HIS- 171 | 3.09 | 160.91 | H-Bond (Protein Donor) |
| C8 | CB | THR- 174 | 4.26 | 0 | Hydrophobic |
| C15 | CG2 | THR- 174 | 3.79 | 0 | Hydrophobic |
| C6 | CG2 | THR- 174 | 3.66 | 0 | Hydrophobic |
| O24 | OG1 | THR- 174 | 2.68 | 156.38 | H-Bond (Protein Donor) |
| O28 | OG1 | THR- 174 | 3.24 | 121.06 | H-Bond (Protein Donor) |
| C19 | CE | MET- 178 | 3.64 | 0 | Hydrophobic |
