sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2005-09-28
| 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 | 100 % |
| B-Factor: | 86.866 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.436 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 68.82 | 31.18 |
| According to VolSite | |
| HET Code: | 3AC |
|---|---|
| Formula: | C17H15IN2O2 |
| Molecular weight: | 406.218 g/mol |
| DrugBank ID: | DB07035 |
| Buried Surface Area: | 67.47 % |
| Polar Surface area: | 62.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 143.439 | -26.293 | 75.0443 |
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 |
| C51 | CB | LEU- 100 | 3.67 | 0 | Hydrophobic |
| C61 | CD1 | LEU- 100 | 3.97 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 100 | 3.54 | 0 | Hydrophobic |
| N14 | O | LYS- 101 | 2.85 | 150.8 | H-Bond (Ligand Donor) |
| I12 | CG1 | VAL- 106 | 3.93 | 0 | Hydrophobic |
| C62 | CG1 | VAL- 106 | 4.33 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 106 | 4.19 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 108 | 4.31 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 108 | 3.78 | 0 | Hydrophobic |
| I12 | CD1 | TYR- 181 | 4.17 | 0 | Hydrophobic |
| I12 | CB | TYR- 188 | 4.14 | 0 | Hydrophobic |
| C27 | CE2 | TYR- 188 | 3.33 | 0 | Hydrophobic |
| C28 | CZ | TYR- 188 | 4.44 | 0 | Hydrophobic |
| C24 | CD1 | TYR- 188 | 3.22 | 0 | Hydrophobic |
| C26 | CB | TYR- 188 | 3.71 | 0 | Hydrophobic |
| C25 | CB | TYR- 188 | 3.9 | 0 | Hydrophobic |
| C28 | CB | PHE- 227 | 3.42 | 0 | Hydrophobic |
| C28 | CB | TRP- 229 | 3.94 | 0 | Hydrophobic |
| C61 | CD2 | LEU- 234 | 4.45 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 234 | 4.06 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 234 | 3.46 | 0 | Hydrophobic |
| C51 | CE1 | TYR- 318 | 3.42 | 0 | Hydrophobic |
| C61 | CZ | TYR- 318 | 4.06 | 0 | Hydrophobic |
