sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.930 Å
X-ray
2015-07-06
| Name: | Protein kinase YopO |
|---|---|
| ID: | Q93KQ6_YEREN |
| AC: | Q93KQ6 |
| Organism: | Yersinia enterocolitica |
| Reign: | Bacteria |
| TaxID: | 630 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 73.168 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.863 | 772.875 |
| % Hydrophobic | % Polar |
|---|---|
| 44.98 | 55.02 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.5 % |
| 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 |
|---|---|---|
| 22.1444 | -1.6877 | 3.87837 |
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 |
| O1B | OG | SER- 144 | 2.64 | 160.72 | H-Bond (Protein Donor) |
| C5' | CD1 | ILE- 146 | 3.94 | 0 | Hydrophobic |
| C4' | CG1 | ILE- 146 | 4.49 | 0 | Hydrophobic |
| C1' | CG1 | ILE- 146 | 4.42 | 0 | Hydrophobic |
| O3B | NZ | LYS- 160 | 3.54 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 160 | 3.08 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 160 | 3.08 | 136.87 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 163 | 3.86 | 0 | Ionic (Protein Cationic) |
| N6 | O | ASP- 212 | 2.75 | 140.04 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 214 | 2.8 | 158.68 | H-Bond (Protein Donor) |
| C2' | CD | ARG- 218 | 4.29 | 0 | Hydrophobic |
| O2' | NH1 | ARG- 218 | 3.37 | 168.76 | H-Bond (Protein Donor) |
| O3' | O | GLY- 271 | 2.8 | 149.11 | H-Bond (Ligand Donor) |
| C2' | CG2 | VAL- 274 | 4.17 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 285 | 3.76 | 0 | Hydrophobic |
| O2B | MG | MG- 802 | 1.96 | 0 | Metal Acceptor |
| O2A | MG | MG- 802 | 1.97 | 0 | Metal Acceptor |
| O3B | O | HOH- 901 | 3.07 | 122.59 | H-Bond (Protein Donor) |
