sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 Å
X-ray
2005-05-26
| Name: | RIO-type serine/threonine-protein kinase Rio1 |
|---|---|
| ID: | RIO1_ARCFU |
| AC: | O28471 |
| Organism: | Archaeoglobus fulgidus |
| Reign: | Archaea |
| TaxID: | 224325 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.760 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.153 | 617.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.91 | 48.09 |
| According to VolSite | |
| HET Code: | XYA |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | DB03528 |
| Buried Surface Area: | 55.87 % |
| Polar Surface area: | 139.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 34.1908 | 21.5375 | 8.43789 |
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 |
| C1' | CG2 | ILE- 55 | 3.46 | 0 | Hydrophobic |
| C4' | CB | SER- 56 | 3.59 | 0 | Hydrophobic |
| N6 | O | GLU- 148 | 2.97 | 149.86 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 150 | 2.74 | 171.09 | H-Bond (Protein Donor) |
| C2' | CE | MET- 203 | 3.63 | 0 | Hydrophobic |
| C5' | CD1 | ILE- 211 | 3.55 | 0 | Hydrophobic |
| C3' | CD1 | ILE- 211 | 4.22 | 0 | Hydrophobic |
