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
2004-09-07
| Name: | Polyphosphate kinase |
|---|---|
| ID: | PPK_ECOLI |
| AC: | P0A7B1 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 31.730 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.014 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 34.96 | 65.04 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 54.06 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| 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 |
|---|---|---|
| -5.57706 | -41.9585 | 58.6607 |
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' | CG2 | ILE- 41 | 4.38 | 0 | Hydrophobic |
| O2B | CZ | ARG- 375 | 2.92 | 0 | Ionic (Protein Cationic) |
| O2G | NE2 | HIS- 435 | 2.68 | 123.65 | H-Bond (Protein Donor) |
| O3G | NE2 | HIS- 435 | 3.01 | 159.95 | H-Bond (Protein Donor) |
| C5' | CZ | TYR- 468 | 4.39 | 0 | Hydrophobic |
| C3' | CZ | TYR- 468 | 3.69 | 0 | Hydrophobic |
| O1A | NH2 | ARG- 564 | 2.67 | 155.34 | H-Bond (Protein Donor) |
| O1A | CZ | ARG- 564 | 3.64 | 0 | Ionic (Protein Cationic) |
| N6 | O | ASP- 587 | 3.27 | 157.91 | H-Bond (Ligand Donor) |
| C3' | CD1 | LEU- 590 | 3.68 | 0 | Hydrophobic |
| O2G | NE2 | HIS- 592 | 3.18 | 126.77 | H-Bond (Protein Donor) |
| O3B | NE2 | HIS- 592 | 2.98 | 152.29 | H-Bond (Protein Donor) |
| O1G | MG | MG- 705 | 1.93 | 0 | Metal Acceptor |
| O2A | MG | MG- 706 | 2.48 | 0 | Metal Acceptor |
