sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 Å
X-ray
2013-10-23
| Name: | D-tyrosyl-tRNA(Tyr) deacylase |
|---|---|
| ID: | Q8IIS0_PLAF7 |
| AC: | Q8IIS0 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 36329 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 23 % |
| B | 77 % |
| B-Factor: | 29.462 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.868 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 57.79 | 42.21 |
| According to VolSite | |
| HET Code: | D3Y |
|---|---|
| Formula: | C19H24N7O5 |
| Molecular weight: | 430.438 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.8 % |
| Polar Surface area: | 196.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -16.6985 | -3.90874 | -1.49526 |
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 |
| N1 | N | ILE- 43 | 3.06 | 165.66 | H-Bond (Protein Donor) |
| N6 | O | ILE- 43 | 3.04 | 168.74 | H-Bond (Ligand Donor) |
| O2' | OG | SER- 87 | 2.65 | 166.58 | H-Bond (Ligand Donor) |
| C2' | CB | SER- 87 | 3.74 | 0 | Hydrophobic |
| O | NE2 | GLN- 88 | 3.11 | 139.88 | H-Bond (Protein Donor) |
| O | N | PHE- 89 | 3.15 | 142.04 | H-Bond (Protein Donor) |
| C5' | CZ | PHE- 89 | 3.65 | 0 | Hydrophobic |
| CB | CG2 | THR- 90 | 4.39 | 0 | Hydrophobic |
| N6 | O | LYS- 107 | 3.1 | 156.49 | H-Bond (Ligand Donor) |
| C2' | CD1 | PHE- 137 | 4.48 | 0 | Hydrophobic |
| C1' | CZ | PHE- 137 | 3.49 | 0 | Hydrophobic |
| O2' | N | GLY- 138 | 2.92 | 176.44 | H-Bond (Protein Donor) |
| N | O | GLY- 149 | 3.16 | 168.15 | H-Bond (Ligand Donor) |
