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
2013-11-13
| 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 | 63 % |
| B | 37 % |
| B-Factor: | 21.370 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.718 | 364.500 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | IY7 |
|---|---|
| Formula: | C27H31N2O7 |
| Molecular weight: | 495.544 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.03 % |
| Polar Surface area: | 155.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -11.6505 | 45.7555 | 11.7578 |
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 |
| C13 | CG | GLN- 95 | 4.01 | 0 | Hydrophobic |
| C13 | CB | ALA- 98 | 4.29 | 0 | Hydrophobic |
| C21 | CD1 | TYR- 99 | 4.27 | 0 | Hydrophobic |
| C22 | CB | TYR- 99 | 4.36 | 0 | Hydrophobic |
| C25 | CB | TYR- 99 | 3.95 | 0 | Hydrophobic |
| C24 | CG | TYR- 99 | 3.97 | 0 | Hydrophobic |
| C14 | CB | TYR- 99 | 4.1 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 102 | 3.76 | 0 | Hydrophobic |
| C9 | CG2 | THR- 125 | 4.15 | 0 | Hydrophobic |
| C12 | CG2 | THR- 125 | 3.78 | 0 | Hydrophobic |
| C3 | CB | ALA- 129 | 3.82 | 0 | Hydrophobic |
| C2 | CB | TRP- 132 | 3.8 | 0 | Hydrophobic |
| O18 | N | GLU- 170 | 3.03 | 159 | H-Bond (Protein Donor) |
| C21 | CB | HIS- 171 | 4.27 | 0 | Hydrophobic |
| O19 | N | HIS- 171 | 3.08 | 157.5 | H-Bond (Protein Donor) |
| O20 | ND1 | HIS- 171 | 3.05 | 166.37 | H-Bond (Protein Donor) |
| C21 | CG | LYS- 173 | 4.08 | 0 | Hydrophobic |
| C24 | CD | LYS- 173 | 4.29 | 0 | Hydrophobic |
| C15 | CB | THR- 174 | 4.41 | 0 | Hydrophobic |
| C4 | CG2 | THR- 174 | 4.19 | 0 | Hydrophobic |
| C16 | CG2 | THR- 174 | 4.16 | 0 | Hydrophobic |
| O19 | OG1 | THR- 174 | 2.64 | 156.35 | H-Bond (Protein Donor) |
| O20 | OG1 | THR- 174 | 3.01 | 120.22 | H-Bond (Protein Donor) |
| C6 | CE | MET- 178 | 3.86 | 0 | Hydrophobic |
| C2 | CE | MET- 178 | 3.3 | 0 | Hydrophobic |
