sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-12-11
| Name: | Choline kinase |
|---|---|
| ID: | Q8IM71_PLAF7 |
| AC: | Q8IM71 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 36329 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.920 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 16 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | ADP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.321 | 685.125 |
| % Hydrophobic | % Polar |
|---|---|
| 35.96 | 64.04 |
| According to VolSite | |
| HET Code: | OPE |
|---|---|
| Formula: | C2H7NO4P |
| Molecular weight: | 140.055 g/mol |
| DrugBank ID: | DB01738 |
| Buried Surface Area: | 55.62 % |
| Polar Surface area: | 109.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 8.2175 | 5.56238 | 10.9594 |
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 |
| N | OD2 | ASP- 288 | 2.68 | 171.74 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 288 | 2.68 | 0 | Ionic (Ligand Cationic) |
| O3 | NE2 | GLN- 290 | 2.71 | 127.9 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 305 | 3.97 | 0 | Ionic (Ligand Cationic) |
| CA | CH2 | TRP- 395 | 3.61 | 0 | Hydrophobic |
| O2 | O | HOH- 456 | 2.73 | 163.33 | H-Bond (Protein Donor) |
