sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-08-17
| Name: | Pol polyprotein |
|---|---|
| ID: | POL_FIVPE |
| AC: | P16088 |
| Organism: | Feline immunodeficiency virus |
| Reign: | Viruses |
| TaxID: | 11674 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 49 % |
| B | 51 % |
| B-Factor: | 27.495 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.437 | 1012.500 |
| % Hydrophobic | % Polar |
|---|---|
| 49.00 | 51.00 |
| According to VolSite | |
| HET Code: | AB1 |
|---|---|
| Formula: | C37H48N4O5 |
| Molecular weight: | 628.801 g/mol |
| DrugBank ID: | DB01601 |
| Buried Surface Area: | 62.81 % |
| Polar Surface area: | 120 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 0.0346522 | 23.2548 | 0.322043 |
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 |
| C5 | CD2 | LEU- 28 | 3.67 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 28 | 3.86 | 0 | Hydrophobic |
| O4 | OD1 | ASP- 30 | 2.61 | 132.22 | H-Bond (Ligand Donor) |
| O4 | OD2 | ASP- 30 | 3.06 | 160.43 | H-Bond (Ligand Donor) |
| N4 | O | GLY- 32 | 3.47 | 158.49 | H-Bond (Ligand Donor) |
| C15 | CB | ALA- 33 | 3.68 | 0 | Hydrophobic |
| C36 | CB | ALA- 33 | 3.39 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 34 | 3.37 | 137.92 | H-Bond (Ligand Donor) |
| O1 | N | ASP- 34 | 3.2 | 164.24 | H-Bond (Protein Donor) |
| C32 | CB | ASP- 34 | 3.77 | 0 | Hydrophobic |
| C31 | CG1 | ILE- 35 | 3.49 | 0 | Hydrophobic |
| C36 | CG2 | VAL- 37 | 3.78 | 0 | Hydrophobic |
| C31 | SD | MET- 56 | 4.19 | 0 | Hydrophobic |
| C37 | CB | MET- 56 | 3.67 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 59 | 3.77 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 59 | 3.58 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 59 | 4.24 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 59 | 4.28 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 99 | 4.32 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 99 | 4.19 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 101 | 3.74 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 101 | 4.02 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 101 | 4.42 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 101 | 3.47 | 0 | Hydrophobic |
| C36 | CD1 | LEU- 101 | 4.06 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 101 | 3.64 | 0 | Hydrophobic |
