sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 Å
X-ray
2008-07-30
| 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 | 100 % |
| B-Factor: | 99.273 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.602 | 695.250 |
| % Hydrophobic | % Polar |
|---|---|
| 62.14 | 37.86 |
| According to VolSite | |
| HET Code: | PZ2 |
|---|---|
| Formula: | C20H14BrN5O |
| Molecular weight: | 420.262 g/mol |
| DrugBank ID: | DB08444 |
| Buried Surface Area: | 72.72 % |
| Polar Surface area: | 87.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 50.4935 | 65.0969 | 16.9996 |
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 |
| C22 | CB | PRO- 95 | 4.38 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 100 | 3.53 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 100 | 3.67 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 100 | 4.35 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 100 | 3.82 | 0 | Hydrophobic |
| N9 | N | LYS- 103 | 3.02 | 169.54 | H-Bond (Protein Donor) |
| C1 | CG2 | VAL- 106 | 4.01 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 106 | 4.44 | 0 | Hydrophobic |
| BR26 | CG2 | VAL- 106 | 3.93 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 106 | 3.83 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 106 | 3.68 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 108 | 4.23 | 0 | Hydrophobic |
| BR26 | CD2 | TYR- 181 | 4.05 | 0 | Hydrophobic |
| C22 | CE1 | TYR- 188 | 3.95 | 0 | Hydrophobic |
| C20 | CB | TYR- 188 | 3.49 | 0 | Hydrophobic |
| C22 | CH2 | TRP- 229 | 3.42 | 0 | Hydrophobic |
| C17 | CB | TRP- 229 | 4.12 | 0 | Hydrophobic |
| C14 | CB | LEU- 234 | 4.28 | 0 | Hydrophobic |
| C15 | CG | LEU- 234 | 4.34 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 234 | 4.39 | 0 | Hydrophobic |
| C27 | CZ | TYR- 318 | 3.55 | 0 | Hydrophobic |
