sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2001-07-16
| 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 | 93 % |
| B | 7 % |
| B-Factor: | 57.701 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.176 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 68.87 | 31.13 |
| According to VolSite | |
| HET Code: | UC1 |
|---|---|
| Formula: | C17H18ClNO2S |
| Molecular weight: | 335.848 g/mol |
| DrugBank ID: | DB05871 |
| Buried Surface Area: | 80.39 % |
| Polar Surface area: | 66.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -0.692 | -35.0178 | 24.318 |
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 |
| CF | CG | PRO- 95 | 3.92 | 0 | Hydrophobic |
| CA | CD2 | LEU- 100 | 3.67 | 0 | Hydrophobic |
| CF | CD2 | LEU- 100 | 4.17 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 100 | 3.53 | 0 | Hydrophobic |
| N | O | LYS- 101 | 2.64 | 149.11 | H-Bond (Ligand Donor) |
| C6 | CG | LYS- 103 | 3.97 | 0 | Hydrophobic |
| CC | CG1 | VAL- 106 | 3.77 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 106 | 3.94 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 106 | 3.97 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 106 | 3.93 | 0 | Hydrophobic |
| CA | CG | GLU- 138 | 4.02 | 0 | Hydrophobic |
| CA | CG1 | VAL- 179 | 4.25 | 0 | Hydrophobic |
| CA | CB | TYR- 181 | 4.1 | 0 | Hydrophobic |
| CF | CD1 | TYR- 181 | 3.41 | 0 | Hydrophobic |
| CC | CB | CSD- 188 | 3.66 | 0 | Hydrophobic |
| CL | CD2 | PHE- 227 | 3.46 | 0 | Hydrophobic |
| CF | CE2 | TRP- 229 | 4.21 | 0 | Hydrophobic |
| CG | CD2 | TRP- 229 | 3.79 | 0 | Hydrophobic |
| CG | CD2 | LEU- 234 | 3.54 | 0 | Hydrophobic |
| CL | CB | LEU- 234 | 3.67 | 0 | Hydrophobic |
| C5 | CB | PRO- 236 | 4.4 | 0 | Hydrophobic |
