sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.730 Å
X-ray
2000-02-03
| 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 | 87 % |
| B | 13 % |
| B-Factor: | 40.320 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.517 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 74.42 | 25.58 |
| According to VolSite | |
| HET Code: | BFU |
|---|---|
| Formula: | C18H17BrFN3O3 |
| Molecular weight: | 422.248 g/mol |
| DrugBank ID: | DB07451 |
| Buried Surface Area: | 80.15 % |
| Polar Surface area: | 91.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -10.0655 | 141.946 | 173.931 |
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 |
| F | CG | PRO- 95 | 3.58 | 0 | Hydrophobic |
| C18 | CB | PRO- 95 | 3.9 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 100 | 3.66 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 100 | 3.53 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 100 | 4.07 | 0 | Hydrophobic |
| N8 | O | LYS- 101 | 2.9 | 161.37 | H-Bond (Ligand Donor) |
| O10 | N | LYS- 101 | 3.26 | 144.47 | H-Bond (Protein Donor) |
| C6 | CB | LYS- 103 | 3.71 | 0 | Hydrophobic |
| BR | CG1 | VAL- 106 | 3.46 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 179 | 3.94 | 0 | Hydrophobic |
| F | CD1 | TYR- 181 | 3.52 | 0 | Hydrophobic |
| C21 | CB | TYR- 181 | 3.96 | 0 | Hydrophobic |
| C16 | CG | TYR- 181 | 3.43 | 0 | Hydrophobic |
| C25 | CD2 | TYR- 188 | 3.68 | 0 | Hydrophobic |
| C26 | CE2 | TYR- 188 | 3.88 | 0 | Hydrophobic |
| C21 | CB | TYR- 188 | 4.16 | 0 | Hydrophobic |
| BR | CB | PRO- 225 | 3.9 | 0 | Hydrophobic |
| BR | CD2 | PHE- 227 | 3.92 | 0 | Hydrophobic |
| C26 | CB | PHE- 227 | 3.53 | 0 | Hydrophobic |
| C25 | CD2 | TRP- 229 | 3.77 | 0 | Hydrophobic |
| C26 | CB | TRP- 229 | 3.91 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 234 | 4.16 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 234 | 4.01 | 0 | Hydrophobic |
| BR | CB | LEU- 234 | 3.89 | 0 | Hydrophobic |
| C13 | CG | GLU- 1138 | 3.91 | 0 | Hydrophobic |
| F | CG | GLU- 1138 | 3.27 | 0 | Hydrophobic |
