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
2013-12-20
| 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 | 43 % |
| B | 57 % |
| B-Factor: | 22.998 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.799 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.75 | 44.25 |
| According to VolSite | |
| HET Code: | RVN |
|---|---|
| Formula: | C17H10NO5 |
| Molecular weight: | 308.265 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.39 % |
| Polar Surface area: | 87.69 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: | 2 |
| X | Y | Z |
|---|---|---|
| -32.7514 | 32.0043 | 0.26487 |
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 |
| C7 | CB | GLN- 95 | 4.48 | 0 | Hydrophobic |
| C7 | CB | ALA- 98 | 4.13 | 0 | Hydrophobic |
| C10 | CD1 | TYR- 99 | 4.19 | 0 | Hydrophobic |
| C8 | CB | TYR- 99 | 4.11 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 102 | 3.72 | 0 | Hydrophobic |
| C6 | CG2 | THR- 125 | 3.69 | 0 | Hydrophobic |
| C21 | CB | ALA- 129 | 3.75 | 0 | Hydrophobic |
| C20 | CB | TRP- 132 | 3.67 | 0 | Hydrophobic |
| O15 | N | GLU- 170 | 2.91 | 161.66 | H-Bond (Protein Donor) |
| O16 | N | HIS- 171 | 2.96 | 163.31 | H-Bond (Protein Donor) |
| C12 | CB | THR- 174 | 4.28 | 0 | Hydrophobic |
| C13 | CG2 | THR- 174 | 4.01 | 0 | Hydrophobic |
| C23 | CG2 | THR- 174 | 3.61 | 0 | Hydrophobic |
| O16 | OG1 | THR- 174 | 2.67 | 162.98 | H-Bond (Protein Donor) |
| C20 | CE | MET- 178 | 3.53 | 0 | Hydrophobic |
