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 | 56 % |
| B | 44 % |
| B-Factor: | 19.445 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.948 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 54.87 | 45.13 |
| According to VolSite | |
| HET Code: | X0P |
|---|---|
| Formula: | C30H30N2O5 |
| Molecular weight: | 498.570 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.43 % |
| Polar Surface area: | 92.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 11.0439 | -46.4564 | 13.9645 |
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 |
| C5 | CG | GLN- 95 | 4.28 | 0 | Hydrophobic |
| C8 | CB | GLN- 95 | 3.96 | 0 | Hydrophobic |
| C8 | CB | ALA- 98 | 4.29 | 0 | Hydrophobic |
| C24 | CB | ALA- 98 | 4.12 | 0 | Hydrophobic |
| C16 | CB | TYR- 99 | 4.23 | 0 | Hydrophobic |
| C22 | CD1 | TYR- 99 | 4.18 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 102 | 3.9 | 0 | Hydrophobic |
| C9 | CG2 | THR- 125 | 4.06 | 0 | Hydrophobic |
| C5 | CG2 | THR- 125 | 3.78 | 0 | Hydrophobic |
| C6 | CB | ALA- 128 | 3.6 | 0 | Hydrophobic |
| C24 | CB | ALA- 129 | 4.01 | 0 | Hydrophobic |
| C18 | CB | ALA- 129 | 4.19 | 0 | Hydrophobic |
| N1 | O | GLN- 168 | 2.75 | 159.91 | H-Bond (Ligand Donor) |
| O1 | N | GLU- 170 | 2.87 | 155.72 | H-Bond (Protein Donor) |
| C4 | CB | GLU- 170 | 4.02 | 0 | Hydrophobic |
| C50 | CB | GLU- 170 | 3.59 | 0 | Hydrophobic |
| O4 | N | HIS- 171 | 2.99 | 163.66 | H-Bond (Protein Donor) |
| C12 | CG2 | THR- 174 | 4.31 | 0 | Hydrophobic |
| C17 | CB | THR- 174 | 4.32 | 0 | Hydrophobic |
| C24 | CG2 | THR- 174 | 4.1 | 0 | Hydrophobic |
| C10 | CG2 | THR- 174 | 3.88 | 0 | Hydrophobic |
| O4 | OG1 | THR- 174 | 2.7 | 168.56 | H-Bond (Protein Donor) |
| C7 | CE | MET- 178 | 3.85 | 0 | Hydrophobic |
