sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2013-12-04
| 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 | 57 % |
| B | 43 % |
| B-Factor: | 25.893 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.589 | 367.875 |
| % Hydrophobic | % Polar |
|---|---|
| 48.62 | 51.38 |
| According to VolSite | |
| HET Code: | CWU |
|---|---|
| Formula: | C18H15O5 |
| Molecular weight: | 311.309 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.45 % |
| Polar Surface area: | 78.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -11.389 | 44.3293 | 12.9465 |
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 | 3.66 | 0 | Hydrophobic |
| C6 | CB | ALA- 98 | 4.21 | 0 | Hydrophobic |
| C15 | CD1 | TYR- 99 | 4.21 | 0 | Hydrophobic |
| C11 | CB | TYR- 99 | 4.16 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 102 | 3.67 | 0 | Hydrophobic |
| C5 | CG2 | THR- 125 | 3.76 | 0 | Hydrophobic |
| C2 | CB | ALA- 129 | 3.79 | 0 | Hydrophobic |
| C3 | CB | TRP- 132 | 3.64 | 0 | Hydrophobic |
| O20 | N | GLU- 170 | 2.89 | 164.76 | H-Bond (Protein Donor) |
| O19 | N | HIS- 171 | 2.98 | 164.04 | H-Bond (Protein Donor) |
| O22 | ND1 | HIS- 171 | 2.99 | 161.12 | H-Bond (Protein Donor) |
| C12 | CB | THR- 174 | 4.23 | 0 | Hydrophobic |
| C4 | CG2 | THR- 174 | 3.48 | 0 | Hydrophobic |
| C7 | CG2 | THR- 174 | 4.02 | 0 | Hydrophobic |
| C9 | CG2 | THR- 174 | 3.72 | 0 | Hydrophobic |
| O19 | OG1 | THR- 174 | 2.73 | 152.79 | H-Bond (Protein Donor) |
| O22 | OG1 | THR- 174 | 2.79 | 120.85 | H-Bond (Protein Donor) |
| C1 | CE | MET- 178 | 3.81 | 0 | Hydrophobic |
| C8 | CE | MET- 178 | 3.26 | 0 | Hydrophobic |
