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
2013-11-11
| 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 | 62 % |
| B | 38 % |
| B-Factor: | 16.852 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.665 | 405.000 |
| % Hydrophobic | % Polar |
|---|---|
| 52.50 | 47.50 |
| According to VolSite | |
| HET Code: | D0T |
|---|---|
| Formula: | C29H29N2O7 |
| Molecular weight: | 517.550 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.61 % |
| Polar Surface area: | 132.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -33.3453 | 32.8604 | -13.8445 |
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 |
| C23 | CG | GLN- 95 | 3.81 | 0 | Hydrophobic |
| C27 | CG | GLN- 95 | 4.32 | 0 | Hydrophobic |
| C11 | CG | GLN- 95 | 3.37 | 0 | Hydrophobic |
| C27 | CG | GLU- 96 | 4.45 | 0 | Hydrophobic |
| C6 | CB | ALA- 98 | 4.49 | 0 | Hydrophobic |
| C17 | CB | ALA- 98 | 4.46 | 0 | Hydrophobic |
| C21 | CD1 | TYR- 99 | 4.36 | 0 | Hydrophobic |
| C23 | CB | TYR- 99 | 4.19 | 0 | Hydrophobic |
| C27 | CB | TYR- 99 | 3.76 | 0 | Hydrophobic |
| C29 | CG | TYR- 99 | 3.8 | 0 | Hydrophobic |
| C11 | CB | TYR- 99 | 4.16 | 0 | Hydrophobic |
| C5 | CG2 | THR- 125 | 4.1 | 0 | Hydrophobic |
| C17 | CG2 | THR- 125 | 4.38 | 0 | Hydrophobic |
| C19 | CB | ALA- 128 | 3.67 | 0 | Hydrophobic |
| C16 | CB | ALA- 129 | 3.65 | 0 | Hydrophobic |
| C20 | CB | TRP- 132 | 4.03 | 0 | Hydrophobic |
| N1 | O | GLN- 168 | 2.85 | 173.39 | H-Bond (Ligand Donor) |
| O4 | N | GLU- 170 | 2.84 | 162.29 | H-Bond (Protein Donor) |
| C4 | CB | GLU- 170 | 4.44 | 0 | Hydrophobic |
| C21 | CB | HIS- 171 | 4.26 | 0 | Hydrophobic |
| O1 | N | HIS- 171 | 2.93 | 162.61 | H-Bond (Protein Donor) |
| C21 | CG | LYS- 173 | 4.23 | 0 | Hydrophobic |
| C29 | CD | LYS- 173 | 4.4 | 0 | Hydrophobic |
| O1 | OG1 | THR- 174 | 2.69 | 164.55 | H-Bond (Protein Donor) |
| C8 | CG2 | THR- 174 | 3.98 | 0 | Hydrophobic |
| C20 | CE | MET- 178 | 3.25 | 0 | Hydrophobic |
