sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2001-07-16
| 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 | 93 % |
| B | 7 % |
| B-Factor: | 69.261 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.011 | 685.125 |
| % Hydrophobic | % Polar |
|---|---|
| 62.07 | 37.93 |
| According to VolSite | |
| HET Code: | FTC |
|---|---|
| Formula: | C15H16ClFN4OS |
| Molecular weight: | 354.830 g/mol |
| DrugBank ID: | DB07797 |
| Buried Surface Area: | 75.67 % |
| Polar Surface area: | 91.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -0.856696 | -34.3869 | 23.7999 |
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 |
| C6 | CB | LEU- 100 | 4.11 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 100 | 4.08 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 100 | 4.23 | 0 | Hydrophobic |
| N8 | O | LYS- 101 | 2.65 | 132.7 | H-Bond (Ligand Donor) |
| F18 | CG1 | VAL- 106 | 3.94 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 106 | 3.7 | 0 | Hydrophobic |
| N14 | OE2 | GLU- 138 | 2.61 | 145.18 | H-Bond (Ligand Donor) |
| N14 | OE1 | GLU- 138 | 3.29 | 145.72 | H-Bond (Ligand Donor) |
| C11 | CG1 | VAL- 179 | 3.37 | 0 | Hydrophobic |
| C12 | CB | CYS- 181 | 3.97 | 0 | Hydrophobic |
| C16 | SG | CYS- 181 | 4.31 | 0 | Hydrophobic |
| C18 | CB | CYS- 181 | 4.36 | 0 | Hydrophobic |
| C12 | CB | TYR- 188 | 4.38 | 0 | Hydrophobic |
| CA | CD2 | TYR- 188 | 4.04 | 0 | Hydrophobic |
| CB | CE2 | TYR- 188 | 3.88 | 0 | Hydrophobic |
| F18 | CG | TYR- 188 | 3.98 | 0 | Hydrophobic |
| C17 | CB | TYR- 188 | 3.34 | 0 | Hydrophobic |
| CL7 | CD2 | PHE- 227 | 4.47 | 0 | Hydrophobic |
| CB | CB | PHE- 227 | 4.1 | 0 | Hydrophobic |
| CB | CE3 | TRP- 229 | 3.47 | 0 | Hydrophobic |
| CL7 | CB | LEU- 234 | 3.51 | 0 | Hydrophobic |
| CB | CD1 | LEU- 234 | 3.68 | 0 | Hydrophobic |
| C5 | CZ | TYR- 318 | 3.32 | 0 | Hydrophobic |
