sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2013-11-22
| 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: | 24.679 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.558 | 418.500 |
| % Hydrophobic | % Polar |
|---|---|
| 49.19 | 50.81 |
| According to VolSite | |
| HET Code: | 8P3 |
|---|---|
| Formula: | C16H12NO3 |
| Molecular weight: | 266.271 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.91 % |
| Polar Surface area: | 60.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 33.6301 | -31.483 | -12.6943 |
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 |
| C16 | CB | GLN- 95 | 4.17 | 0 | Hydrophobic |
| C16 | CB | ALA- 98 | 4.17 | 0 | Hydrophobic |
| C15 | CB | TYR- 99 | 4.19 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 102 | 4.15 | 0 | Hydrophobic |
| C17 | CG2 | THR- 125 | 3.88 | 0 | Hydrophobic |
| C7 | CB | ALA- 128 | 3.53 | 0 | Hydrophobic |
| C1 | CB | ALA- 129 | 4.41 | 0 | Hydrophobic |
| C1 | CB | TRP- 132 | 3.63 | 0 | Hydrophobic |
| O19 | N | GLU- 170 | 2.82 | 162.87 | H-Bond (Protein Donor) |
| O20 | N | HIS- 171 | 2.93 | 163.13 | H-Bond (Protein Donor) |
| C14 | CB | THR- 174 | 4.3 | 0 | Hydrophobic |
| C3 | CG2 | THR- 174 | 3.65 | 0 | Hydrophobic |
| C13 | CG2 | THR- 174 | 3.97 | 0 | Hydrophobic |
| O20 | OG1 | THR- 174 | 2.7 | 171.03 | H-Bond (Protein Donor) |
| C1 | CE | MET- 178 | 3.65 | 0 | Hydrophobic |
| C2 | SD | MET- 178 | 4.39 | 0 | Hydrophobic |
