sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2011-09-08
| Name: | Serine/threonine-protein kinase toxin HipA |
|---|---|
| ID: | HIPA_ECOLI |
| AC: | P23874 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.776 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.906 | 421.875 |
| % Hydrophobic | % Polar |
|---|---|
| 61.60 | 38.40 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 74.05 % |
| 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 |
|---|---|---|
| -1.57233 | 1.38896 | 20.0576 |
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' | CG2 | VAL- 98 | 4.47 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 98 | 3.7 | 0 | Hydrophobic |
| C5' | CG1 | VAL- 151 | 3.86 | 0 | Hydrophobic |
| C4' | CB | ALA- 152 | 4.35 | 0 | Hydrophobic |
| O1B | N | GLN- 155 | 3.04 | 133.84 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 157 | 2.54 | 164.19 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 157 | 2.54 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 181 | 3 | 132.54 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 181 | 2.7 | 139.9 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 181 | 3 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 181 | 2.7 | 0 | Ionic (Protein Cationic) |
| N6 | O | GLU- 234 | 2.8 | 130.8 | H-Bond (Ligand Donor) |
| N1 | N | PHE- 236 | 2.82 | 162.05 | H-Bond (Protein Donor) |
| DuAr | DuAr | PHE- 236 | 3.71 | 0 | Aromatic Face/Face |
| O3' | O | LYS- 313 | 3.24 | 156.39 | H-Bond (Ligand Donor) |
| C3' | CE1 | TYR- 331 | 3.59 | 0 | Hydrophobic |
| O2A | MG | MG- 441 | 2.68 | 0 | Metal Acceptor |
| O2' | O | HOH- 514 | 2.7 | 164.97 | H-Bond (Protein Donor) |
