sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.690 Å
X-ray
2013-07-22
| 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: | 77.715 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.308 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 62.07 | 37.93 |
| According to VolSite | |
| HET Code: | 1YQ |
|---|---|
| Formula: | C21H16ClN3O4 |
| Molecular weight: | 409.822 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.6 % |
| Polar Surface area: | 91.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 496.05 | -24.7488 | 23.1165 |
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 |
| C0E | CD1 | LEU- 100 | 3.62 | 0 | Hydrophobic |
| C0O | CD1 | LEU- 100 | 3.62 | 0 | Hydrophobic |
| C00 | CB | LYS- 103 | 4.49 | 0 | Hydrophobic |
| CL1 | CD | LYS- 103 | 3.89 | 0 | Hydrophobic |
| O10 | N | LYS- 103 | 3.31 | 174.46 | H-Bond (Protein Donor) |
| C0O | CG2 | VAL- 106 | 4.17 | 0 | Hydrophobic |
| C05 | CG2 | VAL- 106 | 3.93 | 0 | Hydrophobic |
| C0H | CG1 | VAL- 106 | 4.15 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 179 | 3.34 | 0 | Hydrophobic |
| C02 | CG2 | VAL- 179 | 3.93 | 0 | Hydrophobic |
| CL1 | CZ | TYR- 181 | 4 | 0 | Hydrophobic |
| C03 | CB | TYR- 188 | 4.38 | 0 | Hydrophobic |
| C0G | CD2 | TYR- 188 | 3.41 | 0 | Hydrophobic |
| C0H | CB | TYR- 188 | 3.51 | 0 | Hydrophobic |
| C0G | CD1 | LEU- 234 | 3.67 | 0 | Hydrophobic |
| C0P | CZ | TYR- 318 | 3.37 | 0 | Hydrophobic |
