sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.110 Å
X-ray
2011-08-18
| Name: | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) |
|---|---|
| ID: | UPPS_ECOLI |
| AC: | P60472 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 2.5.1.31 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 34.783 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.826 | 813.375 |
| % Hydrophobic | % Polar |
|---|---|
| 67.22 | 32.78 |
| According to VolSite | |
| HET Code: | TH9 |
|---|---|
| Formula: | C19H26NO5 |
| Molecular weight: | 348.413 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.53 % |
| Polar Surface area: | 98.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -8.731 | 3.56104 | -0.91684 |
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 |
| CAJ | CE | MET- 25 | 4.33 | 0 | Hydrophobic |
| CAO | CB | MET- 25 | 4.31 | 0 | Hydrophobic |
| CAR | CE | MET- 25 | 4.45 | 0 | Hydrophobic |
| CAF | CB | ASN- 28 | 3.66 | 0 | Hydrophobic |
| OAB | N | GLY- 29 | 2.72 | 152.16 | H-Bond (Protein Donor) |
| OAB | CZ | ARG- 39 | 3.79 | 0 | Ionic (Protein Cationic) |
| OAB | NH2 | ARG- 39 | 3.17 | 131.86 | H-Bond (Protein Donor) |
| CAG | CB | ALA- 47 | 3.47 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 50 | 4.27 | 0 | Hydrophobic |
| CAJ | CG2 | VAL- 50 | 4 | 0 | Hydrophobic |
| CAJ | CB | ALA- 69 | 4.19 | 0 | Hydrophobic |
| CAO | CB | ALA- 69 | 4.29 | 0 | Hydrophobic |
| CAQ | CB | ALA- 69 | 3.5 | 0 | Hydrophobic |
| CAL | CB | ALA- 92 | 4.44 | 0 | Hydrophobic |
| CAA | CG | GLU- 96 | 4.44 | 0 | Hydrophobic |
| CAK | CD1 | ILE- 141 | 4.07 | 0 | Hydrophobic |
| CAN | CG2 | ILE- 141 | 3.61 | 0 | Hydrophobic |
