sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2015-03-04
| Name: | Aprataxin-like protein |
|---|---|
| ID: | APTX_SCHPO |
| AC: | O74859 |
| Organism: | Schizosaccharomyces pombe |
| Reign: | Eukaryota |
| TaxID: | 284812 |
| EC Number: | 3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 36.275 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.374 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 44.83 | 55.17 |
| According to VolSite | |
| HET Code: | GMP |
|---|---|
| Formula: | C10H13N5O5 |
| Molecular weight: | 283.241 g/mol |
| DrugBank ID: | DB02857 |
| Buried Surface Area: | 61.38 % |
| Polar Surface area: | 155.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -27.3871 | 78.5938 | 25.8989 |
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 | OH | TYR- 41 | 3.11 | 153.72 | H-Bond (Protein Donor) |
| N2 | OH | TYR- 41 | 3.48 | 139.35 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 63 | 2.95 | 168.38 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 63 | 3.21 | 168.87 | H-Bond (Ligand Donor) |
| C5' | CG | MET- 143 | 3.4 | 0 | Hydrophobic |
| O5' | NE2 | HIS- 147 | 3.01 | 152.15 | H-Bond (Ligand Donor) |
