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
2008-06-27
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 51.974 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.516 | 526.500 |
| % Hydrophobic | % Polar |
|---|---|
| 68.59 | 31.41 |
| According to VolSite | |
| HET Code: | GFA |
|---|---|
| Formula: | C21H16ClNO3 |
| Molecular weight: | 365.810 g/mol |
| DrugBank ID: | DB07826 |
| Buried Surface Area: | 81.14 % |
| Polar Surface area: | 55.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -3.44904 | -35.0256 | 24.1799 |
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 |
| C8 | CD1 | LEU- 100 | 4.21 | 0 | Hydrophobic |
| C14 | CB | LEU- 100 | 4.07 | 0 | Hydrophobic |
| C13 | CB | LEU- 100 | 3.97 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 100 | 3.53 | 0 | Hydrophobic |
| O3 | N | LYS- 103 | 2.7 | 161.54 | H-Bond (Protein Donor) |
| C12 | CB | LYS- 103 | 4.07 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 106 | 3.54 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 106 | 3.4 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 106 | 4.28 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 106 | 4.46 | 0 | Hydrophobic |
| C20 | CB | VAL- 106 | 4.1 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 106 | 3.65 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 179 | 4.23 | 0 | Hydrophobic |
| CL1 | CB | TYR- 181 | 4.44 | 0 | Hydrophobic |
| CL1 | CB | TYR- 188 | 4.01 | 0 | Hydrophobic |
| C9 | CB | TYR- 188 | 4.16 | 0 | Hydrophobic |
| C4 | CE2 | TYR- 188 | 3.24 | 0 | Hydrophobic |
| C18 | CB | PRO- 225 | 4.21 | 0 | Hydrophobic |
| C19 | CG | PRO- 225 | 4.15 | 0 | Hydrophobic |
| C4 | CB | PHE- 227 | 3.84 | 0 | Hydrophobic |
| C3 | CB | TRP- 229 | 3.81 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 234 | 3.31 | 0 | Hydrophobic |
| C19 | CG | PRO- 236 | 3.67 | 0 | Hydrophobic |
| C14 | CE1 | TYR- 318 | 3.74 | 0 | Hydrophobic |
