sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2009-08-25
| 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 | 89 % |
| B | 11 % |
| B-Factor: | 96.415 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.574 | 1113.750 |
| % Hydrophobic | % Polar |
|---|---|
| 64.24 | 35.76 |
| According to VolSite | |
| HET Code: | AC7 |
|---|---|
| Formula: | C27H26N2O8 |
| Molecular weight: | 506.504 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.39 % |
| Polar Surface area: | 144.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 48.9744 | -29.63 | 39.0732 |
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 |
| C19 | CG | PRO- 95 | 4.1 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 100 | 4.27 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 100 | 4 | 0 | Hydrophobic |
| C22 | CB | LEU- 100 | 4.42 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 106 | 4.48 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 106 | 4.42 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 106 | 3.87 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 108 | 4.22 | 0 | Hydrophobic |
| C21 | CB | GLU- 138 | 4.32 | 0 | Hydrophobic |
| C18 | CD2 | TYR- 181 | 3.46 | 0 | Hydrophobic |
| C19 | CE2 | TYR- 181 | 3.43 | 0 | Hydrophobic |
| C21 | CD1 | TYR- 181 | 4.05 | 0 | Hydrophobic |
| C24 | CB | TYR- 181 | 4.25 | 0 | Hydrophobic |
| C1 | CB | TYR- 188 | 4.27 | 0 | Hydrophobic |
| C18 | CD1 | TYR- 188 | 4.05 | 0 | Hydrophobic |
| C24 | CG | TYR- 188 | 4.39 | 0 | Hydrophobic |
| C13 | CE2 | TYR- 188 | 3.25 | 0 | Hydrophobic |
| C23 | CB | LYS- 223 | 3.74 | 0 | Hydrophobic |
| C25 | CB | LYS- 223 | 3.45 | 0 | Hydrophobic |
| C23 | CB | PHE- 227 | 3.79 | 0 | Hydrophobic |
| C25 | CE2 | PHE- 227 | 3.5 | 0 | Hydrophobic |
| C14 | CB | PHE- 227 | 4.12 | 0 | Hydrophobic |
| C10 | CB | PHE- 227 | 3.84 | 0 | Hydrophobic |
| C17 | CE2 | TRP- 229 | 3.52 | 0 | Hydrophobic |
| C18 | CZ2 | TRP- 229 | 3.95 | 0 | Hydrophobic |
| C19 | CH2 | TRP- 229 | 4.04 | 0 | Hydrophobic |
| C12 | CB | TRP- 229 | 3.41 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 234 | 4.19 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 234 | 3.57 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 234 | 4.14 | 0 | Hydrophobic |
| C22 | CE1 | TYR- 318 | 4.04 | 0 | Hydrophobic |
| N69 | OH | TYR- 318 | 3.02 | 149.27 | H-Bond (Protein Donor) |
