sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.980 Å
X-ray
2009-06-25
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 69.953 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.440 | 654.750 |
| % Hydrophobic | % Polar |
|---|---|
| 66.49 | 33.51 |
| According to VolSite | |
| HET Code: | RT3 |
|---|---|
| Formula: | C19H20ClN3O4S2 |
| Molecular weight: | 453.963 g/mol |
| DrugBank ID: | DB08494 |
| Buried Surface Area: | 65.69 % |
| Polar Surface area: | 143.25 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 8.56776 | 10.77 | 15.4148 |
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 |
| S12 | CB | LEU- 100 | 4.05 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 100 | 3.61 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 100 | 4.09 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 100 | 4.42 | 0 | Hydrophobic |
| O29 | N | LYS- 103 | 2.88 | 151.31 | H-Bond (Protein Donor) |
| C13 | CG | LYS- 103 | 3.6 | 0 | Hydrophobic |
| N29 | O | LYS- 104 | 2.6 | 156.6 | H-Bond (Ligand Donor) |
| O30 | N | VAL- 106 | 2.53 | 168.11 | H-Bond (Protein Donor) |
| CL22 | CG1 | VAL- 106 | 3.68 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 106 | 4.08 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 106 | 3.23 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 106 | 3.23 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 179 | 3.56 | 0 | Hydrophobic |
| C27 | CD2 | TYR- 181 | 3.61 | 0 | Hydrophobic |
| C10 | CB | TYR- 181 | 3.53 | 0 | Hydrophobic |
| C5 | CB | TYR- 181 | 3.36 | 0 | Hydrophobic |
| C27 | CD1 | TYR- 188 | 3.62 | 0 | Hydrophobic |
| C10 | CB | TYR- 188 | 3.78 | 0 | Hydrophobic |
| C20 | CG | PRO- 225 | 4.13 | 0 | Hydrophobic |
| CL22 | CE2 | PHE- 227 | 4.09 | 0 | Hydrophobic |
| C27 | CD2 | TRP- 229 | 3.6 | 0 | Hydrophobic |
| CL22 | CB | LEU- 234 | 4.39 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 234 | 3.49 | 0 | Hydrophobic |
| N15 | O | HIS- 235 | 3.46 | 135.86 | H-Bond (Ligand Donor) |
| C19 | CB | PRO- 236 | 4.05 | 0 | Hydrophobic |
