sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2013-11-25
| 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 | 54 % |
| B | 46 % |
| B-Factor: | 26.121 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.827 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.75 | 44.25 |
| According to VolSite | |
| HET Code: | NZL |
|---|---|
| Formula: | C24H28N2O5 |
| Molecular weight: | 424.490 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.38 % |
| Polar Surface area: | 115.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -33.7547 | 32.3581 | -14.7965 |
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 |
| C4 | CG | GLN- 95 | 3.49 | 0 | Hydrophobic |
| C3 | CB | ALA- 98 | 4.28 | 0 | Hydrophobic |
| C8 | CD1 | TYR- 99 | 4.24 | 0 | Hydrophobic |
| C5 | CB | TYR- 99 | 4.12 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 102 | 3.64 | 0 | Hydrophobic |
| C3 | CG2 | THR- 125 | 3.8 | 0 | Hydrophobic |
| C10 | CG2 | THR- 125 | 4.44 | 0 | Hydrophobic |
| C27 | CB | ALA- 129 | 3.6 | 0 | Hydrophobic |
| C28 | CB | TRP- 132 | 3.74 | 0 | Hydrophobic |
| N21 | O | ASP- 167 | 2.93 | 174.21 | H-Bond (Ligand Donor) |
| N13 | O | GLN- 168 | 2.81 | 159.07 | H-Bond (Ligand Donor) |
| C18 | CB | GLU- 170 | 3.97 | 0 | Hydrophobic |
| O30 | N | GLU- 170 | 2.91 | 161.41 | H-Bond (Protein Donor) |
| O31 | N | HIS- 171 | 2.95 | 154.88 | H-Bond (Protein Donor) |
| C1 | CG2 | THR- 174 | 4.15 | 0 | Hydrophobic |
| C6 | CB | THR- 174 | 4.34 | 0 | Hydrophobic |
| C25 | CG2 | THR- 174 | 3.54 | 0 | Hydrophobic |
| O31 | OG1 | THR- 174 | 2.75 | 156.96 | H-Bond (Protein Donor) |
| C23 | CE | MET- 178 | 3.61 | 0 | Hydrophobic |
