sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2012-01-12
| Name: | Choline kinase alpha |
|---|---|
| ID: | CHKA_HUMAN |
| AC: | P35790 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.1.32 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 35.219 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.092 | 320.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.21 | 55.79 |
| According to VolSite | |
| HET Code: | 0H7 |
|---|---|
| Formula: | C16H18Cl2NOS2 |
| Molecular weight: | 375.356 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.75 % |
| Polar Surface area: | 81.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 8.49282 | 25.9234 | 27.3314 |
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 |
| N5 | OD2 | ASP- 306 | 3.92 | 0 | Ionic (Ligand Cationic) |
| N5 | OD1 | ASP- 306 | 2.83 | 0 | Ionic (Ligand Cationic) |
| N5 | OD1 | ASP- 306 | 2.83 | 140.97 | H-Bond (Ligand Donor) |
| N5 | OE2 | GLU- 349 | 3.94 | 0 | Ionic (Ligand Cationic) |
| C3 | CZ | TYR- 354 | 4.33 | 0 | Hydrophobic |
| C9 | CZ | TYR- 354 | 4.39 | 0 | Hydrophobic |
| S22 | CB | TYR- 354 | 3.91 | 0 | Hydrophobic |
| S22 | CD2 | TYR- 354 | 3.41 | 0 | Hydrophobic |
| C7 | CE3 | TRP- 420 | 3.7 | 0 | Hydrophobic |
| C9 | CD2 | TRP- 420 | 4.31 | 0 | Hydrophobic |
| C7 | CH2 | TRP- 423 | 3.43 | 0 | Hydrophobic |
| C8 | CZ3 | TRP- 423 | 3.68 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 433 | 3.62 | 0 | Hydrophobic |
| CL1 | CB | PHE- 435 | 3.4 | 0 | Hydrophobic |
| CL1 | CZ | TYR- 437 | 3.28 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 440 | 3.75 | 0 | Hydrophobic |
| N5 | O | HOH- 704 | 3.33 | 145.26 | H-Bond (Ligand Donor) |
