sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2011-06-15
| Name: | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) |
|---|---|
| ID: | UPPS_ECOL6 |
| AC: | P60473 |
| Organism: | Escherichia coli O6:H1 |
| Reign: | Bacteria |
| TaxID: | 199310 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 34.432 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.331 | 1485.000 |
| % Hydrophobic | % Polar |
|---|---|
| 58.64 | 41.36 |
| According to VolSite | |
| HET Code: | P09 |
|---|---|
| Formula: | C22H18NO4 |
| Molecular weight: | 360.383 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.4 % |
| Polar Surface area: | 78.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -12.8241 | 3.03044 | 3.69807 |
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 |
| CAM | CE | MET- 25 | 4.49 | 0 | Hydrophobic |
| CAJ | CG1 | VAL- 50 | 3.92 | 0 | Hydrophobic |
| CAM | CG2 | VAL- 50 | 4.37 | 0 | Hydrophobic |
| CAX | CB | ALA- 69 | 3.84 | 0 | Hydrophobic |
| CAF | CG1 | VAL- 82 | 4.15 | 0 | Hydrophobic |
| NAQ | O | LEU- 85 | 3.13 | 164.46 | H-Bond (Ligand Donor) |
| CAZ | CB | LEU- 85 | 3.64 | 0 | Hydrophobic |
| CAG | SD | MET- 86 | 3.87 | 0 | Hydrophobic |
| CAO | CD2 | LEU- 88 | 3.9 | 0 | Hydrophobic |
| CAB | CE1 | PHE- 89 | 4.03 | 0 | Hydrophobic |
| CAI | CB | PHE- 89 | 4.41 | 0 | Hydrophobic |
| CAK | CB | PHE- 89 | 4.37 | 0 | Hydrophobic |
| CAL | CB | PHE- 89 | 3.9 | 0 | Hydrophobic |
| CAP | CB | ALA- 92 | 3.46 | 0 | Hydrophobic |
| CAB | CB | LEU- 93 | 3.99 | 0 | Hydrophobic |
| CAA | CB | GLU- 96 | 4.04 | 0 | Hydrophobic |
| CAA | CD1 | LEU- 100 | 4.07 | 0 | Hydrophobic |
| CAA | CG1 | ILE- 141 | 3.95 | 0 | Hydrophobic |
| CAN | CG2 | ILE- 141 | 3.92 | 0 | Hydrophobic |
| CAJ | CD1 | ILE- 141 | 3.71 | 0 | Hydrophobic |
| CAP | CG2 | ILE- 141 | 3.72 | 0 | Hydrophobic |
| OAD | N | ASN- 144 | 3.03 | 156 | H-Bond (Protein Donor) |
| CAF | CB | ASN- 144 | 4.1 | 0 | Hydrophobic |
