sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.930 Å
X-ray
2014-12-26
| Name: | Carbohydrate/pyrimidine kinase, PfkB family |
|---|---|
| ID: | Q5JDA3_THEKO |
| AC: | Q5JDA3 |
| Organism: | Thermococcus kodakarensis ) |
| Reign: | Archaea |
| TaxID: | 69014 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 35.776 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.619 | 972.000 |
| % Hydrophobic | % Polar |
|---|---|
| 39.93 | 60.07 |
| According to VolSite | |
| HET Code: | ACP |
|---|---|
| Formula: | C11H14N5O12P3 |
| Molecular weight: | 501.176 g/mol |
| DrugBank ID: | DB03909 |
| Buried Surface Area: | 70.06 % |
| Polar Surface area: | 310.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 5.45019 | 36.379 | -13.0662 |
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 |
| O3G | CZ | ARG- 85 | 3.02 | 0 | Ionic (Protein Cationic) |
| O2B | OD2 | ASP- 166 | 2.7 | 154.64 | H-Bond (Protein Donor) |
| O1A | OG | SER- 187 | 2.56 | 153.38 | H-Bond (Protein Donor) |
| C5' | CB | SER- 187 | 3.9 | 0 | Hydrophobic |
| O1A | N | GLY- 189 | 2.85 | 159.82 | H-Bond (Protein Donor) |
| C2' | CG | PRO- 206 | 3.75 | 0 | Hydrophobic |
| N6 | O | VAL- 209 | 3.45 | 142.09 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 209 | 3.28 | 137 | H-Bond (Protein Donor) |
| O3G | OG | SER- 214 | 3.07 | 156.56 | H-Bond (Protein Donor) |
| O1G | N | GLY- 218 | 2.72 | 160.82 | H-Bond (Protein Donor) |
| C5' | CB | PHE- 221 | 3.88 | 0 | Hydrophobic |
| C4' | CG | PHE- 221 | 3.75 | 0 | Hydrophobic |
| C4' | CG2 | THR- 245 | 4.34 | 0 | Hydrophobic |
| C1' | CG2 | THR- 245 | 3.7 | 0 | Hydrophobic |
| O1B | MG | MG- 303 | 1.96 | 0 | Metal Acceptor |
| O3' | O | HOH- 419 | 2.77 | 175.22 | H-Bond (Ligand Donor) |
