sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2008-06-27
| 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 | 95 % |
| B | 5 % |
| B-Factor: | 49.041 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.425 | 590.625 |
| % Hydrophobic | % Polar |
|---|---|
| 68.00 | 32.00 |
| According to VolSite | |
| HET Code: | GWE |
|---|---|
| Formula: | C23H19ClF4N2O5S |
| Molecular weight: | 546.919 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.34 % |
| Polar Surface area: | 121.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -3.68178 | -34.4926 | 24.5437 |
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 |
| F2 | CB | PRO- 95 | 3.45 | 0 | Hydrophobic |
| C6 | CB | LEU- 100 | 4.16 | 0 | Hydrophobic |
| C15 | CB | LEU- 100 | 3.96 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 100 | 3.92 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 100 | 3.72 | 0 | Hydrophobic |
| F2 | CD2 | LEU- 100 | 3.7 | 0 | Hydrophobic |
| O3 | N | LYS- 103 | 3.06 | 168.9 | H-Bond (Protein Donor) |
| C5 | CG | LYS- 103 | 4.03 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 106 | 3.48 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 106 | 3.77 | 0 | Hydrophobic |
| C20 | CB | VAL- 106 | 4.08 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 106 | 3.3 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 106 | 3.78 | 0 | Hydrophobic |
| N2 | O | VAL- 106 | 3.24 | 128.38 | H-Bond (Ligand Donor) |
| CL1 | CG2 | VAL- 179 | 3.84 | 0 | Hydrophobic |
| CL1 | CD1 | TYR- 181 | 3.54 | 0 | Hydrophobic |
| F3 | CD1 | TYR- 181 | 3.35 | 0 | Hydrophobic |
| F1 | CB | TYR- 183 | 3.93 | 0 | Hydrophobic |
| C3 | CB | TYR- 188 | 4.04 | 0 | Hydrophobic |
| CL1 | CB | TYR- 188 | 3.98 | 0 | Hydrophobic |
| C13 | CB | TYR- 188 | 4.35 | 0 | Hydrophobic |
| F1 | CE1 | TYR- 188 | 3.39 | 0 | Hydrophobic |
| F4 | CE2 | TYR- 188 | 3.51 | 0 | Hydrophobic |
| F3 | CD1 | TYR- 188 | 3.84 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 188 | 3.93 | 0 | Aromatic Face/Face |
| C19 | CG | PRO- 225 | 4.2 | 0 | Hydrophobic |
| C23 | CD2 | PHE- 227 | 3.65 | 0 | Hydrophobic |
| F4 | CB | PHE- 227 | 3.52 | 0 | Hydrophobic |
| F1 | CH2 | TRP- 229 | 3.49 | 0 | Hydrophobic |
| F4 | CE3 | TRP- 229 | 3.47 | 0 | Hydrophobic |
| F2 | CZ2 | TRP- 229 | 3.79 | 0 | Hydrophobic |
| C23 | CB | LEU- 234 | 4.12 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 234 | 3.41 | 0 | Hydrophobic |
| C19 | CG | PRO- 236 | 3.98 | 0 | Hydrophobic |
| C20 | CB | PRO- 236 | 4.07 | 0 | Hydrophobic |
| C15 | CD1 | TYR- 318 | 3.51 | 0 | Hydrophobic |
