sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2010-07-14
| Name: | Serine/threonine-protein kinase CtkA |
|---|---|
| ID: | CTKA_HELPJ |
| AC: | Q9ZKJ5 |
| Organism: | Helicobacter pylori |
| Reign: | Bacteria |
| TaxID: | 85963 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 49.737 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.335 | 2295.000 |
| % Hydrophobic | % Polar |
|---|---|
| 34.26 | 65.74 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.63 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 17.7 | -2.31442 | 34.259 |
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 |
| C1' | CD1 | PHE- 17 | 4.26 | 0 | Hydrophobic |
| C4' | CB | PHE- 17 | 4.36 | 0 | Hydrophobic |
| O1B | NZ | LYS- 24 | 2.76 | 145.33 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 24 | 2.76 | 0 | Ionic (Protein Cationic) |
| C5' | CD | LYS- 24 | 4.47 | 0 | Hydrophobic |
| C5' | SD | MET- 35 | 3.73 | 0 | Hydrophobic |
| C1' | SD | MET- 35 | 4.49 | 0 | Hydrophobic |
| O1A | NZ | LYS- 37 | 2.54 | 151.56 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 37 | 2.54 | 0 | Ionic (Protein Cationic) |
| N6 | OE1 | GLN- 72 | 3.13 | 171.78 | H-Bond (Ligand Donor) |
| N6 | O | LYS- 88 | 3.07 | 161.59 | H-Bond (Ligand Donor) |
| N1 | N | PHE- 90 | 2.94 | 161.39 | H-Bond (Protein Donor) |
| C2' | CD2 | LEU- 97 | 3.65 | 0 | Hydrophobic |
| O1G | NE2 | HIS- 157 | 3.43 | 158.51 | H-Bond (Protein Donor) |
| C3' | CE2 | PHE- 178 | 3.9 | 0 | Hydrophobic |
| O1G | MG | MG- 405 | 2.3 | 0 | Metal Acceptor |
| O3A | MG | MG- 405 | 2.32 | 0 | Metal Acceptor |
