sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2013-11-11
| 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: | 18.709 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.844 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 49.61 | 50.39 |
| According to VolSite | |
| HET Code: | ZSW |
|---|---|
| Formula: | C28H33N2O7 |
| Molecular weight: | 509.571 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.33 % |
| Polar Surface area: | 132.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -33.7171 | 33.3683 | -13.5971 |
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 | CG | GLN- 95 | 3.5 | 0 | Hydrophobic |
| C6 | CB | ALA- 98 | 4.32 | 0 | Hydrophobic |
| C23 | CD1 | TYR- 99 | 4.2 | 0 | Hydrophobic |
| C25 | CB | TYR- 99 | 4.24 | 0 | Hydrophobic |
| C29 | CB | TYR- 99 | 3.76 | 0 | Hydrophobic |
| C31 | CG | TYR- 99 | 3.87 | 0 | Hydrophobic |
| C11 | CB | TYR- 99 | 4.13 | 0 | Hydrophobic |
| C5 | CG2 | THR- 125 | 4.44 | 0 | Hydrophobic |
| C18 | CB | ALA- 128 | 4.37 | 0 | Hydrophobic |
| C22 | CB | ALA- 128 | 4.1 | 0 | Hydrophobic |
| C22 | CZ3 | TRP- 131 | 4.25 | 0 | Hydrophobic |
| C18 | CB | TRP- 132 | 4.41 | 0 | Hydrophobic |
| N32 | O | GLN- 168 | 2.75 | 141.68 | H-Bond (Ligand Donor) |
| O37 | N | GLU- 170 | 2.9 | 167.22 | H-Bond (Protein Donor) |
| C23 | CB | HIS- 171 | 4.23 | 0 | Hydrophobic |
| O34 | N | HIS- 171 | 2.92 | 165.35 | H-Bond (Protein Donor) |
| C23 | CG | LYS- 173 | 3.93 | 0 | Hydrophobic |
| C31 | CD | LYS- 173 | 4.25 | 0 | Hydrophobic |
| C12 | CB | THR- 174 | 4.23 | 0 | Hydrophobic |
| C19 | CG2 | THR- 174 | 4.19 | 0 | Hydrophobic |
| C8 | CG2 | THR- 174 | 4.03 | 0 | Hydrophobic |
| O34 | OG1 | THR- 174 | 2.71 | 161.66 | H-Bond (Protein Donor) |
| C19 | CE | MET- 178 | 3.31 | 0 | Hydrophobic |
