sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 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: | 23.722 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.439 | 2065.500 |
| % Hydrophobic | % Polar |
|---|---|
| 32.19 | 67.81 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.25 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -1.09685 | 32.1643 | 11.2189 |
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 |
| C4' | CB | PHE- 17 | 4.47 | 0 | Hydrophobic |
| C1' | CD1 | PHE- 17 | 4.2 | 0 | Hydrophobic |
| O1B | ND2 | ASN- 21 | 3.48 | 152.01 | H-Bond (Protein Donor) |
| O2B | N | ASN- 21 | 2.95 | 126.97 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 24 | 2.81 | 158.83 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 24 | 2.81 | 0 | Ionic (Protein Cationic) |
| C5' | SD | MET- 35 | 4.44 | 0 | Hydrophobic |
| C1' | SD | MET- 35 | 4.1 | 0 | Hydrophobic |
| O1B | NZ | LYS- 37 | 3.87 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 37 | 2.78 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 37 | 2.78 | 163.14 | H-Bond (Protein Donor) |
| N6 | OE1 | GLN- 72 | 2.81 | 156.77 | H-Bond (Ligand Donor) |
| N6 | O | LYS- 88 | 3.04 | 154.39 | H-Bond (Ligand Donor) |
| N1 | N | PHE- 90 | 2.95 | 164.58 | H-Bond (Protein Donor) |
| DuAr | DuAr | PHE- 90 | 3.64 | 0 | Aromatic Face/Face |
| C2' | CD2 | LEU- 97 | 3.33 | 0 | Hydrophobic |
| C3' | CE2 | PHE- 178 | 4.07 | 0 | Hydrophobic |
| O3B | MG | MG- 400 | 2.35 | 0 | Metal Acceptor |
| O2A | MG | MG- 400 | 2.28 | 0 | Metal Acceptor |
