sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
1997-05-15
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1A2 |
| AC: | P03369 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11685 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 51 % |
| B | 49 % |
| B-Factor: | 10.277 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.105 | 853.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.64 | 53.36 |
| According to VolSite | |
| HET Code: | ARQ |
|---|---|
| Formula: | C30H38N3O4 |
| Molecular weight: | 504.640 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.31 % |
| Polar Surface area: | 87.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 5.24397 | -1.71008 | 13.7661 |
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 |
| C11 | CD1 | LEU- 23 | 3.7 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 23 | 3.91 | 0 | Hydrophobic |
| O1 | OD2 | ASP- 25 | 3.02 | 154.33 | H-Bond (Ligand Donor) |
| N1 | O | GLY- 27 | 3.24 | 154.31 | H-Bond (Ligand Donor) |
| C3 | CB | ALA- 28 | 3.94 | 0 | Hydrophobic |
| C3 | CB | ASP- 30 | 4.32 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 32 | 4.2 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 47 | 4.05 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 47 | 3.81 | 0 | Hydrophobic |
| C2 | CG1 | ILE- 50 | 4.13 | 0 | Hydrophobic |
| C29 | CD1 | ILE- 50 | 3.84 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 50 | 3.64 | 0 | Hydrophobic |
| C25 | CG1 | ILE- 50 | 3.35 | 0 | Hydrophobic |
| O2 | N | ILE- 50 | 2.96 | 157.48 | H-Bond (Protein Donor) |
| C18 | CG | PRO- 81 | 4.01 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 82 | 3.84 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 82 | 4.23 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 84 | 4.06 | 0 | Hydrophobic |
