sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.450 Å
X-ray
2011-06-15
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 41.675 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.762 | 911.250 |
| % Hydrophobic | % Polar |
|---|---|
| 66.30 | 33.70 |
| According to VolSite | |
| HET Code: | 0FW |
|---|---|
| Formula: | C27H17NO6 |
| Molecular weight: | 451.427 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.76 % |
| Polar Surface area: | 118.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -12.5287 | 8.76521 | 2.86629 |
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 |
| CAH | CB | ALA- 47 | 3.78 | 0 | Hydrophobic |
| CAP | CG1 | VAL- 50 | 3.66 | 0 | Hydrophobic |
| CAT | CG | ARG- 51 | 4.11 | 0 | Hydrophobic |
| CAO | CB | ARG- 51 | 3.74 | 0 | Hydrophobic |
| CBC | CG1 | VAL- 54 | 4.29 | 0 | Hydrophobic |
| CAT | CG1 | VAL- 54 | 3.68 | 0 | Hydrophobic |
| CAU | CB | SER- 55 | 3.78 | 0 | Hydrophobic |
| CAS | CB | ALA- 58 | 3.37 | 0 | Hydrophobic |
| OAD | ND2 | ASN- 59 | 3.21 | 152.19 | H-Bond (Protein Donor) |
| CAG | CE3 | TRP- 91 | 3.3 | 0 | Hydrophobic |
| CAR | CB | ALA- 92 | 4.06 | 0 | Hydrophobic |
| CAL | CB | ALA- 92 | 3.7 | 0 | Hydrophobic |
| CAL | CG | GLU- 96 | 4.33 | 0 | Hydrophobic |
| CAO | CG | GLU- 96 | 3.6 | 0 | Hydrophobic |
| NAV | OE1 | GLU- 96 | 2.75 | 148.96 | H-Bond (Ligand Donor) |
| CAI | CB | SER- 99 | 3.9 | 0 | Hydrophobic |
| CAT | CD2 | LEU- 100 | 3.56 | 0 | Hydrophobic |
| CAJ | CD2 | LEU- 100 | 3.49 | 0 | Hydrophobic |
| CAK | CB | HIS- 103 | 3.93 | 0 | Hydrophobic |
| CAS | CB | HIS- 103 | 3.85 | 0 | Hydrophobic |
| CAN | CG2 | VAL- 105 | 3.85 | 0 | Hydrophobic |
