sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2007-09-27
| 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 | 96 % |
| B | 4 % |
| B-Factor: | 36.227 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.641 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 74.26 | 25.74 |
| According to VolSite | |
| HET Code: | MRX |
|---|---|
| Formula: | C13H14BrN3O3S |
| Molecular weight: | 372.238 g/mol |
| DrugBank ID: | DB08211 |
| Buried Surface Area: | 76.8 % |
| Polar Surface area: | 104.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 10.0572 | 13.9884 | 16.6214 |
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 |
| C14 | CG | PRO- 95 | 4.3 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 100 | 4.26 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 100 | 4.2 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 100 | 3.41 | 0 | Hydrophobic |
| N9 | O | LYS- 101 | 2.74 | 144.11 | H-Bond (Ligand Donor) |
| O19 | N | LYS- 101 | 2.91 | 164.62 | H-Bond (Protein Donor) |
| C4 | CB | LYS- 103 | 4.15 | 0 | Hydrophobic |
| C3 | CD | LYS- 103 | 4.28 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 106 | 4.41 | 0 | Hydrophobic |
| BR | CG1 | VAL- 106 | 3.37 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 106 | 3.57 | 0 | Hydrophobic |
| C15 | CG | TYR- 181 | 3.82 | 0 | Hydrophobic |
| C14 | CD2 | TYR- 181 | 3.71 | 0 | Hydrophobic |
| C13 | CG | TYR- 188 | 4.25 | 0 | Hydrophobic |
| C12 | CD2 | TYR- 188 | 4.04 | 0 | Hydrophobic |
| BR | CD2 | PHE- 227 | 3.62 | 0 | Hydrophobic |
| C14 | CH2 | TRP- 229 | 3.88 | 0 | Hydrophobic |
| C13 | CD2 | TRP- 229 | 4.05 | 0 | Hydrophobic |
| BR | CB | LEU- 234 | 3.66 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 234 | 3.84 | 0 | Hydrophobic |
