sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2015-07-30
| 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 | 93 % |
| B | 7 % |
| B-Factor: | 47.013 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.732 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 74.77 | 25.23 |
| According to VolSite | |
| HET Code: | T27 |
|---|---|
| Formula: | C22H18N6 |
| Molecular weight: | 366.419 g/mol |
| DrugBank ID: | DB08864 |
| Buried Surface Area: | 77.34 % |
| Polar Surface area: | 97.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 50.1021 | -27.6581 | 36.5428 |
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 |
| C7 | CG | PRO- 95 | 3.97 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 100 | 3.83 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 100 | 4.05 | 0 | Hydrophobic |
| C16 | CB | LEU- 100 | 4.23 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 100 | 4.07 | 0 | Hydrophobic |
| N2 | N | LYS- 101 | 3.18 | 170.32 | H-Bond (Protein Donor) |
| N4 | O | LYS- 101 | 2.55 | 154.56 | H-Bond (Ligand Donor) |
| C15 | CG | LYS- 103 | 3.66 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 106 | 3.95 | 0 | Hydrophobic |
| C10 | CG | GLU- 138 | 4.17 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 179 | 3.72 | 0 | Hydrophobic |
| C10 | CB | VAL- 179 | 3.89 | 0 | Hydrophobic |
| C7 | CD1 | TYR- 181 | 3.56 | 0 | Hydrophobic |
| C2 | CD2 | TYR- 181 | 3.31 | 0 | Hydrophobic |
| C5 | CB | TYR- 181 | 3.64 | 0 | Hydrophobic |
| C6 | CB | TYR- 181 | 3.35 | 0 | Hydrophobic |
| C4 | CB | TYR- 188 | 3.41 | 0 | Hydrophobic |
| C13 | CB | LEU- 234 | 4.37 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 234 | 4.25 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 234 | 4.3 | 0 | Hydrophobic |
