sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2008-07-04
| Name: | Pol protein |
|---|---|
| ID: | A7YKL0_9HIV1 |
| AC: | A7YKL0 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 55.612 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.896 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 74.66 | 25.34 |
| According to VolSite | |
| HET Code: | GWI |
|---|---|
| Formula: | C26H21Cl2N3O6S |
| Molecular weight: | 574.432 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.36 % |
| Polar Surface area: | 150.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -5.92771 | -35.7003 | 24.447 |
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 |
| CL1 | CB | PRO- 95 | 4.37 | 0 | Hydrophobic |
| CL1 | CD1 | ILE- 100 | 4.1 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 100 | 4.15 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 100 | 3.84 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 100 | 3.4 | 0 | Hydrophobic |
| O3 | N | LYS- 103 | 2.95 | 163.43 | H-Bond (Protein Donor) |
| C5 | CG | LYS- 103 | 3.92 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 106 | 3.65 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 106 | 3.83 | 0 | Hydrophobic |
| C20 | CB | VAL- 106 | 4.06 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 106 | 3.66 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 106 | 3.69 | 0 | Hydrophobic |
| O5 | N | VAL- 106 | 3.41 | 158.95 | H-Bond (Protein Donor) |
| CL | CG1 | VAL- 179 | 4.33 | 0 | Hydrophobic |
| CL | CD2 | TYR- 181 | 4.21 | 0 | Hydrophobic |
| CL1 | CD1 | TYR- 181 | 3.55 | 0 | Hydrophobic |
| C3 | CB | TYR- 188 | 4.29 | 0 | Hydrophobic |
| CL | CB | TYR- 188 | 4.39 | 0 | Hydrophobic |
| CL1 | CD1 | TYR- 188 | 3.61 | 0 | Hydrophobic |
| C11 | CD1 | TYR- 188 | 3.41 | 0 | Hydrophobic |
| C10 | CB | TYR- 188 | 4.32 | 0 | Hydrophobic |
| C19 | CB | PRO- 225 | 4.23 | 0 | Hydrophobic |
| C23 | CE2 | PHE- 227 | 3.86 | 0 | Hydrophobic |
| CL1 | CH2 | TRP- 229 | 3.78 | 0 | Hydrophobic |
| C12 | CB | TRP- 229 | 4.42 | 0 | Hydrophobic |
| C23 | CB | LEU- 234 | 4.16 | 0 | Hydrophobic |
| C24 | CG | PRO- 236 | 3.8 | 0 | Hydrophobic |
| C20 | CB | PRO- 236 | 4.02 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 318 | 3.66 | 0 | Hydrophobic |
