sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2011-12-07
| 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 |
|---|---|
| A | 3 % |
| B | 97 % |
| B-Factor: | 36.282 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.733 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 43.56 | 56.44 |
| According to VolSite | |
| HET Code: | 0CK |
|---|---|
| Formula: | C19H20FN5 |
| Molecular weight: | 337.394 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.89 % |
| 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 |
|---|---|---|
| -0.52072 | 5.4002 | -4.2996 |
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 |
| C17 | CG2 | ILE- 15 | 3.86 | 0 | Hydrophobic |
| C16 | CG1 | ILE- 23 | 4.09 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 23 | 3.72 | 0 | Hydrophobic |
| C10 | CB | ALA- 36 | 3.85 | 0 | Hydrophobic |
| C6 | CB | ALA- 36 | 4.12 | 0 | Hydrophobic |
| C1 | CB | LYS- 38 | 3.63 | 0 | Hydrophobic |
| C3 | CD | LYS- 38 | 3.88 | 0 | Hydrophobic |
| C1 | CB | LYS- 38 | 3.63 | 0 | Hydrophobic |
| F1 | CD1 | ILE- 68 | 3.7 | 0 | Hydrophobic |
| C2 | CB | MET- 80 | 4.03 | 0 | Hydrophobic |
| C3 | SD | MET- 80 | 4.3 | 0 | Hydrophobic |
| F1 | CG | MET- 80 | 3.46 | 0 | Hydrophobic |
| C10 | SD | MET- 82 | 3.41 | 0 | Hydrophobic |
| C3 | CE | MET- 82 | 3.57 | 0 | Hydrophobic |
| F1 | CB | MET- 82 | 3.6 | 0 | Hydrophobic |
| N4 | N | LEU- 85 | 2.94 | 158.39 | H-Bond (Protein Donor) |
| N1 | O | LEU- 85 | 3.17 | 145.4 | H-Bond (Ligand Donor) |
| C19 | CB | SER- 88 | 3.51 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 135 | 4.19 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 135 | 4.01 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 135 | 4.05 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 148 | 4.22 | 0 | Hydrophobic |
| N3 | O | HOH- 401 | 2.67 | 179.97 | H-Bond (Protein Donor) |
