sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
1996-12-10
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV2RO |
| AC: | P04584 |
| Organism: | Human immunodeficiency virus type 2 subtype A |
| Reign: | Viruses |
| TaxID: | 11720 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 43 % |
| B | 57 % |
| B-Factor: | 13.478 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.186 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.86 | 51.14 |
| According to VolSite | |
| HET Code: | UIN |
|---|---|
| Formula: | C20H23O3 |
| Molecular weight: | 311.395 g/mol |
| DrugBank ID: | DB08686 |
| Buried Surface Area: | 58.01 % |
| Polar Surface area: | 49.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -0.953696 | 18.496 | 20.1792 |
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 |
| CG3 | CD2 | LEU- 23 | 4.03 | 0 | Hydrophobic |
| CD5 | CD2 | LEU- 23 | 3.76 | 0 | Hydrophobic |
| OA6 | OD1 | ASP- 25 | 3.12 | 123.33 | H-Bond (Ligand Donor) |
| OA6 | OD1 | ASP- 25 | 3.37 | 121.5 | H-Bond (Ligand Donor) |
| CD6 | CB | ALA- 28 | 3.83 | 0 | Hydrophobic |
| CB2 | CB | ALA- 28 | 3.98 | 0 | Hydrophobic |
| OA2 | N | ILE- 50 | 2.9 | 167.46 | H-Bond (Protein Donor) |
| CB5 | CD1 | ILE- 50 | 3.67 | 0 | Hydrophobic |
| CD2 | CG2 | ILE- 50 | 4.24 | 0 | Hydrophobic |
| CD4 | CG2 | ILE- 50 | 3.91 | 0 | Hydrophobic |
| CB4 | CG1 | ILE- 50 | 3.83 | 0 | Hydrophobic |
| CD4 | CG2 | ILE- 82 | 4.06 | 0 | Hydrophobic |
| CG2 | CD1 | ILE- 82 | 3.29 | 0 | Hydrophobic |
| CG3 | CG2 | ILE- 84 | 3.59 | 0 | Hydrophobic |
| CD4 | CD1 | ILE- 84 | 3.93 | 0 | Hydrophobic |
