sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.480 Å
X-ray
2013-03-21
| Name: | Casein kinase II subunit alpha |
|---|---|
| ID: | CSK21_YEAST |
| AC: | P15790 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.720 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.820 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 48.95 | 51.05 |
| According to VolSite | |
| HET Code: | GNP |
|---|---|
| Formula: | C10H13N6O13P3 |
| Molecular weight: | 518.164 g/mol |
| DrugBank ID: | DB02082 |
| Buried Surface Area: | 57.69 % |
| Polar Surface area: | 338.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 23.7353 | -8.04578 | 3.72288 |
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 | VAL- 46 | 4 | 0 | Hydrophobic |
| O1B | N | SER- 52 | 3.46 | 153.52 | H-Bond (Protein Donor) |
| O1B | OG | SER- 52 | 2.54 | 151.38 | H-Bond (Protein Donor) |
| C1' | CG1 | VAL- 54 | 4.44 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 54 | 3.56 | 0 | Hydrophobic |
| O2B | NZ | LYS- 69 | 3.35 | 135.93 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 69 | 3.33 | 152.62 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 69 | 3.35 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 69 | 3.33 | 0 | Ionic (Protein Cationic) |
| O6 | N | VAL- 155 | 2.99 | 162.92 | H-Bond (Protein Donor) |
| N1 | O | VAL- 155 | 2.74 | 147.39 | H-Bond (Ligand Donor) |
| N2 | O | VAL- 155 | 3.35 | 126.29 | H-Bond (Ligand Donor) |
| O1G | NZ | LYS- 197 | 3.41 | 139 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 197 | 3.41 | 0 | Ionic (Protein Cationic) |
| O3' | O | HIS- 199 | 2.73 | 166.46 | H-Bond (Ligand Donor) |
| C2' | CE | MET- 202 | 3.92 | 0 | Hydrophobic |
| C3' | CD1 | ILE- 213 | 3.94 | 0 | Hydrophobic |
| O1G | MG | MG- 402 | 2.21 | 0 | Metal Acceptor |
| O2A | MG | MG- 402 | 1.94 | 0 | Metal Acceptor |
| N2 | O | HOH- 651 | 3.25 | 120.93 | H-Bond (Ligand Donor) |
