sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2003-05-29
| Name: | 2-dehydro-3-deoxyphosphooctonate aldolase |
|---|---|
| ID: | KDSA_ECOLI |
| AC: | P0A715 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 2.5.1.55 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 61.040 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.109 | 678.375 |
| % Hydrophobic | % Polar |
|---|---|
| 44.78 | 55.22 |
| According to VolSite | |
| HET Code: | FPE |
|---|---|
| Formula: | C3H3FO6P |
| Molecular weight: | 185.024 g/mol |
| DrugBank ID: | DB03113 |
| Buried Surface Area: | 64.4 % |
| Polar Surface area: | 122.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 3.938 | -8.49382 | 41.6141 |
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 |
| O3 | N | ALA- 116 | 3.34 | 125.01 | H-Bond (Protein Donor) |
| O4 | N | ALA- 116 | 2.58 | 143.6 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 168 | 3.26 | 0 | Ionic (Protein Cationic) |
| F1 | CD | ARG- 168 | 3.23 | 0 | Hydrophobic |
| F1 | CB | HIS- 202 | 3.74 | 0 | Hydrophobic |
