sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.070 Å
X-ray
2012-10-19
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 41.918 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.123 | 533.250 |
| % Hydrophobic | % Polar |
|---|---|
| 55.70 | 44.30 |
| According to VolSite | |
| HET Code: | 16W |
|---|---|
| Formula: | C17H18ClN5O2 |
| Molecular weight: | 359.810 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.69 % |
| Polar Surface area: | 88.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -40.208 | -19.3748 | 17.8886 |
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 |
| C14 | CG2 | ILE- 15 | 4.31 | 0 | Hydrophobic |
| C15 | CB | ILE- 15 | 4.05 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 15 | 4.29 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 23 | 4.23 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 23 | 3.94 | 0 | Hydrophobic |
| C15 | CB | ILE- 23 | 4.19 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 23 | 3.33 | 0 | Hydrophobic |
| C3 | CB | ALA- 36 | 4.12 | 0 | Hydrophobic |
| C9 | CB | ALA- 36 | 4.22 | 0 | Hydrophobic |
| CL1 | CD | LYS- 38 | 3.59 | 0 | Hydrophobic |
| C6 | CD | LYS- 38 | 3.59 | 0 | Hydrophobic |
| C4 | CB | LYS- 38 | 3.46 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 49 | 4.35 | 0 | Hydrophobic |
| CL1 | CG | GLU- 52 | 4.46 | 0 | Hydrophobic |
| CL1 | CE2 | TYR- 56 | 3.91 | 0 | Hydrophobic |
| C4 | CG | MET- 80 | 4.26 | 0 | Hydrophobic |
| CL1 | CE | MET- 80 | 3.48 | 0 | Hydrophobic |
| C5 | CE | MET- 80 | 3.47 | 0 | Hydrophobic |
| C12 | SD | MET- 82 | 3.83 | 0 | Hydrophobic |
| CL1 | CE | MET- 82 | 4.41 | 0 | Hydrophobic |
| C3 | CB | MET- 82 | 3.65 | 0 | Hydrophobic |
| C1 | CE | MET- 82 | 3.59 | 0 | Hydrophobic |
| N3 | O | GLU- 83 | 3.09 | 176.17 | H-Bond (Ligand Donor) |
| N4 | N | LEU- 85 | 2.87 | 169.26 | H-Bond (Protein Donor) |
| C9 | CD2 | LEU- 135 | 3.9 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 135 | 3.98 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 148 | 3.92 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 148 | 4.21 | 0 | Hydrophobic |
