sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 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 | 26 % |
| B | 74 % |
| B-Factor: | 41.188 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.804 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 48.37 | 51.63 |
| According to VolSite | |
| HET Code: | D3Y |
|---|---|
| Formula: | C19H24N7O5 |
| Molecular weight: | 430.438 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.66 % |
| 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 |
|---|---|---|
| 31.6567 | -3.08397 | 9.48429 |
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 | 3.22 | 170.6 | H-Bond (Protein Donor) |
| N6 | O | ILE- 43 | 3.16 | 170.72 | H-Bond (Ligand Donor) |
| C2' | CB | SER- 87 | 4.16 | 0 | Hydrophobic |
| O2' | OG | SER- 87 | 3.15 | 166.49 | H-Bond (Protein Donor) |
| O | NE2 | GLN- 88 | 3.18 | 139.41 | H-Bond (Protein Donor) |
| O | N | PHE- 89 | 3.02 | 151.27 | H-Bond (Protein Donor) |
| C5' | CE2 | PHE- 89 | 4.34 | 0 | Hydrophobic |
| CD1 | CE2 | PHE- 89 | 3.33 | 0 | Hydrophobic |
| CB | CG2 | THR- 90 | 4.15 | 0 | Hydrophobic |
| N6 | O | LYS- 107 | 2.77 | 150.73 | H-Bond (Ligand Donor) |
| C1' | CZ | PHE- 137 | 3.46 | 0 | Hydrophobic |
| O2' | N | GLY- 138 | 3.15 | 167.62 | H-Bond (Protein Donor) |
| N | O | GLY- 149 | 3 | 161.23 | H-Bond (Ligand Donor) |
| CD2 | CG2 | VAL- 151 | 4.23 | 0 | Hydrophobic |
| CB | CG2 | VAL- 151 | 4.25 | 0 | Hydrophobic |
