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
1996-03-16
| 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: | 25.552 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.525 | 455.625 |
| % Hydrophobic | % Polar |
|---|---|
| 72.59 | 27.41 |
| According to VolSite | |
| HET Code: | MKC |
|---|---|
| Formula: | C17H22N2O3 |
| Molecular weight: | 302.368 g/mol |
| DrugBank ID: | DB08188 |
| Buried Surface Area: | 77.2 % |
| Polar Surface area: | 58.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -1.82805 | -34.3949 | 24.9663 |
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 |
| C17 | CD1 | LEU- 100 | 3.46 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 100 | 3.63 | 0 | Hydrophobic |
| N10 | O | LYS- 101 | 2.75 | 159.62 | H-Bond (Ligand Donor) |
| C13 | CG1 | VAL- 106 | 3.69 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 106 | 4.1 | 0 | Hydrophobic |
| C19 | CB | VAL- 106 | 4 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 106 | 3.58 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 179 | 4.21 | 0 | Hydrophobic |
| C16 | CB | TYR- 181 | 3.43 | 0 | Hydrophobic |
| C2 | CD2 | TYR- 188 | 3.27 | 0 | Hydrophobic |
| C1 | CB | TYR- 188 | 3.9 | 0 | Hydrophobic |
| C16 | CB | TYR- 188 | 3.91 | 0 | Hydrophobic |
| C19 | CG | PRO- 225 | 3.96 | 0 | Hydrophobic |
| C18 | CD2 | PHE- 227 | 4.05 | 0 | Hydrophobic |
| C19 | CE2 | PHE- 227 | 3.6 | 0 | Hydrophobic |
| C2 | CB | PHE- 227 | 4.37 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 234 | 4.46 | 0 | Hydrophobic |
| C17 | CB | LEU- 234 | 3.61 | 0 | Hydrophobic |
| C18 | CB | LEU- 234 | 4.03 | 0 | Hydrophobic |
| C19 | CB | PRO- 236 | 4.45 | 0 | Hydrophobic |
| C17 | CZ | TYR- 318 | 4.41 | 0 | Hydrophobic |
