sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2006-07-13
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1H2 |
| AC: | P04585 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11706 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 96 % |
| B | 4 % |
| B-Factor: | 53.871 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.388 | 2166.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.85 | 43.15 |
| According to VolSite | |
| HET Code: | PC0 |
|---|---|
| Formula: | C16H19FN4OS |
| Molecular weight: | 334.412 g/mol |
| DrugBank ID: | DB08372 |
| Buried Surface Area: | 71.61 % |
| Polar Surface area: | 91.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 1.21583 | -36.9271 | 21.4382 |
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 |
| N8 | O | LYS- 101 | 3.08 | 156.62 | H-Bond (Ligand Donor) |
| C6 | CG | LYS- 103 | 3.91 | 0 | Hydrophobic |
| CL7 | CG1 | VAL- 106 | 4.38 | 0 | Hydrophobic |
| F18 | CG1 | VAL- 106 | 4.24 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 106 | 3.92 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 179 | 3.28 | 0 | Hydrophobic |
| C12 | CB | TYR- 181 | 4.12 | 0 | Hydrophobic |
| CB | CD2 | TYR- 188 | 3.66 | 0 | Hydrophobic |
| F18 | CB | TYR- 188 | 3.31 | 0 | Hydrophobic |
| CL7 | CE2 | PHE- 227 | 3.56 | 0 | Hydrophobic |
| CB | CE2 | PHE- 227 | 4.41 | 0 | Hydrophobic |
| CA | CE3 | TRP- 229 | 3.94 | 0 | Hydrophobic |
| CB | CD2 | TRP- 229 | 3.82 | 0 | Hydrophobic |
| CL7 | CB | LEU- 234 | 3.7 | 0 | Hydrophobic |
| CB | CD1 | LEU- 234 | 3.69 | 0 | Hydrophobic |
