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
2000-12-13
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 87 % |
| B | 13 % |
| B-Factor: | 61.846 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.561 | 594.000 |
| % Hydrophobic | % Polar |
|---|---|
| 68.75 | 31.25 |
| According to VolSite | |
| HET Code: | AAP |
|---|---|
| Formula: | C17H16Cl2N2O2 |
| Molecular weight: | 351.227 g/mol |
| DrugBank ID: | DB07332 |
| Buried Surface Area: | 72.07 % |
| Polar Surface area: | 72.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 142.674 | -26.7144 | 73.3037 |
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 |
| C3' | CB | PRO- 95 | 4.36 | 0 | Hydrophobic |
| CM' | CB | PRO- 95 | 4.07 | 0 | Hydrophobic |
| CL2 | CD1 | LEU- 100 | 3.94 | 0 | Hydrophobic |
| CM' | CD2 | LEU- 100 | 4.29 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 100 | 4.36 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 100 | 3.7 | 0 | Hydrophobic |
| CL6 | CG1 | VAL- 106 | 3.77 | 0 | Hydrophobic |
| CL2 | CG1 | VAL- 179 | 4.27 | 0 | Hydrophobic |
| CM' | CG | TYR- 181 | 3.51 | 0 | Hydrophobic |
| C2' | CB | TYR- 181 | 3.45 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 181 | 3.96 | 0 | Aromatic Face/Face |
| CA | CB | TYR- 188 | 3.57 | 0 | Hydrophobic |
| CL6 | CG | TYR- 188 | 3.85 | 0 | Hydrophobic |
| CM5 | CD2 | TYR- 188 | 3.24 | 0 | Hydrophobic |
| C6' | CD2 | TYR- 188 | 3.22 | 0 | Hydrophobic |
| C6' | CB | TYR- 188 | 3.47 | 0 | Hydrophobic |
| CL6 | CD2 | PHE- 227 | 4.16 | 0 | Hydrophobic |
| CM5 | CD2 | TRP- 229 | 3.46 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 234 | 4.29 | 0 | Hydrophobic |
| C5 | CB | LEU- 234 | 4.11 | 0 | Hydrophobic |
| CL6 | CD1 | LEU- 234 | 4.14 | 0 | Hydrophobic |
| CM5 | CD1 | LEU- 234 | 3.43 | 0 | Hydrophobic |
