sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-06-09
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1N5 |
| AC: | P12497 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11698 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.619 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.219 | 725.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.23 | 49.77 |
| According to VolSite | |
| HET Code: | CIW |
|---|---|
| Formula: | C17H11ClNO5 |
| Molecular weight: | 344.726 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.7 % |
| Polar Surface area: | 78.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 10.153 | -27.0007 | -10.1683 |
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 |
| CL24 | CB | GLN- 62 | 3.9 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 77 | 4.37 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 77 | 3.74 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 77 | 3.74 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 79 | 4.22 | 0 | Hydrophobic |
| CL24 | CG2 | VAL- 79 | 4.01 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 84 | 3.52 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 150 | 3.48 | 0 | Hydrophobic |
| C22 | CG | MET- 154 | 3.74 | 0 | Hydrophobic |
| C3 | SD | MET- 154 | 3.84 | 0 | Hydrophobic |
| C14 | SD | MET- 154 | 3.41 | 0 | Hydrophobic |
| C16 | CG | MET- 154 | 3.37 | 0 | Hydrophobic |
| C22 | CG | GLU- 157 | 3.85 | 0 | Hydrophobic |
| C22 | CG | LEU- 158 | 3.46 | 0 | Hydrophobic |
| C22 | CB | HIS- 183 | 4.45 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 183 | 3.92 | 0 | Aromatic Face/Face |
