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
2001-07-12
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 55.705 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.115 | 273.375 |
| % Hydrophobic | % Polar |
|---|---|
| 69.14 | 30.86 |
| According to VolSite | |
| HET Code: | EFZ |
|---|---|
| Formula: | C14H9ClF3NO2 |
| Molecular weight: | 315.675 g/mol |
| DrugBank ID: | DB00625 |
| Buried Surface Area: | 81.99 % |
| Polar Surface area: | 38.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -0.622952 | -34.7017 | 23.2208 |
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 |
| C2 | CB | LEU- 100 | 4.15 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 100 | 3.97 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 100 | 3.82 | 0 | Hydrophobic |
| O1 | N | LYS- 101 | 3.3 | 177.77 | H-Bond (Protein Donor) |
| N | O | LYS- 101 | 2.67 | 147.1 | H-Bond (Ligand Donor) |
| F3 | CG | LYS- 103 | 3.8 | 0 | Hydrophobic |
| C2 | CG | LYS- 103 | 4.05 | 0 | Hydrophobic |
| CL | CG1 | VAL- 106 | 3.96 | 0 | Hydrophobic |
| F2 | CG1 | VAL- 106 | 3.53 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 106 | 3.89 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 106 | 3.8 | 0 | Hydrophobic |
| F3 | CB | VAL- 179 | 4.19 | 0 | Hydrophobic |
| F1 | CG1 | VAL- 179 | 3.6 | 0 | Hydrophobic |
| F1 | CB | CYS- 181 | 3.9 | 0 | Hydrophobic |
| C10 | SG | CYS- 181 | 3.87 | 0 | Hydrophobic |
| C9 | CB | CYS- 181 | 3.96 | 0 | Hydrophobic |
| C10 | CG | TYR- 188 | 3.35 | 0 | Hydrophobic |
| F2 | CB | TYR- 188 | 3.55 | 0 | Hydrophobic |
| C9 | CB | TYR- 188 | 3.57 | 0 | Hydrophobic |
| CL | CD2 | PHE- 227 | 3.88 | 0 | Hydrophobic |
| C10 | CZ3 | TRP- 229 | 4.37 | 0 | Hydrophobic |
| CL | CB | LEU- 234 | 3.58 | 0 | Hydrophobic |
