sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2013-04-23
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 35.184 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.397 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 62.99 | 37.01 |
| According to VolSite | |
| HET Code: | 1QM |
|---|---|
| Formula: | C18H18FN4O |
| Molecular weight: | 325.360 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.45 % |
| Polar Surface area: | 56.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 21.606 | -46.3424 | 7.27029 |
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 | CD1 | ILE- 15 | 4.03 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 15 | 4.11 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 23 | 3.96 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 23 | 3.81 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 23 | 4.34 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 23 | 3.71 | 0 | Hydrophobic |
| C2 | CB | ALA- 36 | 3.75 | 0 | Hydrophobic |
| C11 | CB | ALA- 36 | 3.67 | 0 | Hydrophobic |
| C8 | CD | LYS- 38 | 3.82 | 0 | Hydrophobic |
| C9 | CB | LYS- 38 | 3.56 | 0 | Hydrophobic |
| F1 | CE | MET- 80 | 3.38 | 0 | Hydrophobic |
| C2 | SD | MET- 82 | 3.64 | 0 | Hydrophobic |
| C10 | CB | MET- 82 | 3.71 | 0 | Hydrophobic |
| F1 | CB | MET- 82 | 3.49 | 0 | Hydrophobic |
| C6 | SD | MET- 82 | 4.14 | 0 | Hydrophobic |
| C8 | CE | MET- 82 | 3.23 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 85 | 4.28 | 0 | Hydrophobic |
| N1 | N | LEU- 85 | 2.97 | 158.45 | H-Bond (Protein Donor) |
| N4 | O | GLY- 86 | 3.07 | 142.4 | H-Bond (Ligand Donor) |
| C16 | CD1 | LEU- 135 | 3.97 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 135 | 3.63 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 148 | 3.46 | 0 | Hydrophobic |
