sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2011-12-06
| Name: | Casein kinase I isoform delta |
|---|---|
| ID: | KC1D_HUMAN |
| AC: | P48730 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 33.166 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.086 | 617.625 |
| % Hydrophobic | % Polar |
|---|---|
| 46.99 | 53.01 |
| According to VolSite | |
| HET Code: | 0CK |
|---|---|
| Formula: | C19H20FN5 |
| Molecular weight: | 337.394 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.59 % |
| Polar Surface area: | 69.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 26.0453 | 38.95 | -13.5535 |
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 |
| C16 | CG2 | ILE- 23 | 4.24 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 23 | 3.73 | 0 | Hydrophobic |
| C10 | CB | ALA- 36 | 3.84 | 0 | Hydrophobic |
| C6 | CB | ALA- 36 | 3.89 | 0 | Hydrophobic |
| C1 | CB | LYS- 38 | 3.94 | 0 | Hydrophobic |
| C3 | CD | LYS- 38 | 4.44 | 0 | Hydrophobic |
| C1 | CB | LYS- 38 | 3.94 | 0 | Hydrophobic |
| F1 | CD1 | ILE- 68 | 4.46 | 0 | Hydrophobic |
| F1 | CE | MET- 80 | 3.5 | 0 | Hydrophobic |
| C10 | SD | MET- 82 | 3.55 | 0 | Hydrophobic |
| F1 | CE | MET- 82 | 3.83 | 0 | Hydrophobic |
| C3 | CE | MET- 82 | 3.42 | 0 | Hydrophobic |
| C1 | CG | MET- 82 | 3.74 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 85 | 4.49 | 0 | Hydrophobic |
| N4 | N | LEU- 85 | 2.99 | 154.6 | H-Bond (Protein Donor) |
| N1 | O | LEU- 85 | 3.29 | 144.49 | H-Bond (Ligand Donor) |
| C19 | CB | SER- 88 | 3.91 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 135 | 4.26 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 135 | 4.42 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 148 | 4.26 | 0 | Hydrophobic |
| N3 | O | HOH- 451 | 3.06 | 161.3 | H-Bond (Protein Donor) |
