sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.840 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 |
|---|---|
| B | 100 % |
| B-Factor: | 34.389 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.320 | 1488.375 |
| % Hydrophobic | % Polar |
|---|---|
| 60.77 | 39.23 |
| According to VolSite | |
| HET Code: | SAX |
|---|---|
| Formula: | C19H29O4 |
| Molecular weight: | 321.431 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.66 % |
| Polar Surface area: | 69.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -13.1986 | 3.78622 | 3.64926 |
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 |
| C12 | CE | MET- 25 | 4.18 | 0 | Hydrophobic |
| C17 | CB | ALA- 47 | 3.82 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 50 | 3.92 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 50 | 4.18 | 0 | Hydrophobic |
| C18 | CG | ARG- 51 | 3.93 | 0 | Hydrophobic |
| C10 | CB | ALA- 69 | 4.03 | 0 | Hydrophobic |
| C12 | CB | ALA- 69 | 4.29 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 82 | 4.16 | 0 | Hydrophobic |
| C7 | CB | LEU- 85 | 4.21 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 85 | 4.13 | 0 | Hydrophobic |
| C5 | CB | LEU- 85 | 3.95 | 0 | Hydrophobic |
| C6 | CB | LEU- 85 | 3.59 | 0 | Hydrophobic |
| C4 | CE | MET- 86 | 3.67 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 88 | 4.14 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 88 | 3.77 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 88 | 3.82 | 0 | Hydrophobic |
| C5 | CB | PHE- 89 | 4.4 | 0 | Hydrophobic |
| C7 | CB | PHE- 89 | 3.89 | 0 | Hydrophobic |
| C9 | CB | PHE- 89 | 3.99 | 0 | Hydrophobic |
| C17 | CZ3 | TRP- 91 | 3.83 | 0 | Hydrophobic |
| C17 | CB | ALA- 92 | 4.35 | 0 | Hydrophobic |
| C14 | CB | ALA- 92 | 3.79 | 0 | Hydrophobic |
| C18 | CG | GLU- 96 | 3.86 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 141 | 3.69 | 0 | Hydrophobic |
| C7 | CB | ALA- 143 | 3.85 | 0 | Hydrophobic |
| O2 | N | ASN- 144 | 3.4 | 153.24 | H-Bond (Protein Donor) |
| O3 | N | ASN- 144 | 2.96 | 132.78 | H-Bond (Protein Donor) |
| C1 | CB | ASN- 144 | 3.87 | 0 | Hydrophobic |
