sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2006-07-12
| 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 | 92 % |
| B | 8 % |
| B-Factor: | 45.596 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.138 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 58.29 | 41.71 |
| According to VolSite | |
| HET Code: | NVP |
|---|---|
| Formula: | C15H14N4O |
| Molecular weight: | 266.298 g/mol |
| DrugBank ID: | DB00238 |
| Buried Surface Area: | 78.27 % |
| Polar Surface area: | 58.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 1.7758 | -36.638 | 21.6635 |
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 |
| C5 | CG | PRO- 95 | 4.32 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 100 | 4.49 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 100 | 3.95 | 0 | Hydrophobic |
| CC | CG | LYS- 103 | 4.43 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 106 | 3.89 | 0 | Hydrophobic |
| CB | CG1 | VAL- 179 | 3.6 | 0 | Hydrophobic |
| CB | CB | TYR- 181 | 4.2 | 0 | Hydrophobic |
| CD | CD1 | TYR- 181 | 4.1 | 0 | Hydrophobic |
| C5 | CD1 | TYR- 181 | 3.33 | 0 | Hydrophobic |
| C5 | CB | TYR- 181 | 3.9 | 0 | Hydrophobic |
| CB | CB | TYR- 188 | 4.1 | 0 | Hydrophobic |
| CD | CD2 | TYR- 188 | 3.98 | 0 | Hydrophobic |
| CD | CD2 | TRP- 229 | 3.8 | 0 | Hydrophobic |
| CD | CD1 | LEU- 234 | 4.08 | 0 | Hydrophobic |
| N14 | O | HOH- 1079 | 2.72 | 179.99 | H-Bond (Protein Donor) |
