sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.820 Å
X-ray
2007-11-08
| 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 | 85 % |
| B | 15 % |
| B-Factor: | 46.689 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.634 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 74.05 | 25.95 |
| According to VolSite | |
| HET Code: | NNI |
|---|---|
| Formula: | C17H13IN2O3S |
| Molecular weight: | 452.266 g/mol |
| DrugBank ID: | DB08284 |
| Buried Surface Area: | 77.38 % |
| Polar Surface area: | 90.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 11.3115 | 63.6706 | 60.3295 |
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 | CG | PRO- 95 | 3.81 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 100 | 3.77 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 100 | 4.07 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 100 | 4.43 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 100 | 4.04 | 0 | Hydrophobic |
| N2 | O | LYS- 101 | 2.78 | 170.57 | H-Bond (Ligand Donor) |
| C12 | CG | LYS- 103 | 3.91 | 0 | Hydrophobic |
| I15 | CG1 | VAL- 106 | 3.64 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 106 | 3.65 | 0 | Hydrophobic |
| C10 | CB | VAL- 179 | 4.31 | 0 | Hydrophobic |
| C2 | CB | TYR- 181 | 3.88 | 0 | Hydrophobic |
| C6 | CB | TYR- 188 | 3.73 | 0 | Hydrophobic |
| I15 | CD1 | PHE- 227 | 3.34 | 0 | Hydrophobic |
| C4 | CE3 | TRP- 229 | 3.4 | 0 | Hydrophobic |
| I15 | CB | LEU- 234 | 3.87 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 234 | 3.22 | 0 | Hydrophobic |
