sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2006-09-12
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 91.654 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.678 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 65.33 | 34.67 |
| According to VolSite | |
| HET Code: | HBY |
|---|---|
| Formula: | C15H20N2O3S2 |
| Molecular weight: | 340.461 g/mol |
| DrugBank ID: | DB07885 |
| Buried Surface Area: | 66.78 % |
| Polar Surface area: | 108.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 141.374 | -24.4969 | 70.76 |
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 |
| C3 | CB | LEU- 100 | 3.98 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 100 | 4.24 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 100 | 3.29 | 0 | Hydrophobic |
| N2 | O | LYS- 101 | 3.06 | 126.01 | H-Bond (Ligand Donor) |
| C8 | CB | ASN- 103 | 4.25 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 106 | 4.25 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 106 | 3.53 | 0 | Hydrophobic |
| S2 | CG1 | VAL- 106 | 4.44 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 106 | 3.52 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 179 | 3.85 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 179 | 3.55 | 0 | Hydrophobic |
| C10 | CD2 | TYR- 188 | 4.41 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 188 | 3.39 | 0 | Hydrophobic |
| S2 | CB | TYR- 188 | 3.8 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 227 | 3.98 | 0 | Hydrophobic |
| C11 | CE2 | TRP- 229 | 3.63 | 0 | Hydrophobic |
| C12 | CZ3 | TRP- 229 | 3.5 | 0 | Hydrophobic |
| C15 | CB | LEU- 234 | 4.05 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 234 | 3.96 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 234 | 3.86 | 0 | Hydrophobic |
