sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.930 Å
X-ray
2012-09-13
| 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 | 96 % |
| B | 4 % |
| B-Factor: | 37.563 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.783 | 1127.250 |
| % Hydrophobic | % Polar |
|---|---|
| 63.47 | 36.53 |
| According to VolSite | |
| HET Code: | 0YZ |
|---|---|
| Formula: | C20H27O5 |
| Molecular weight: | 347.425 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 43.25 % |
| Polar Surface area: | 86.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| 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 |
|---|---|---|
| 43.9823 | 38.912 | 51.7014 |
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 |
| CAA | CB | ALA- 47 | 3.77 | 0 | Hydrophobic |
| CAM | CG1 | VAL- 50 | 4.28 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 50 | 4.46 | 0 | Hydrophobic |
| CAA | CG | ARG- 51 | 4.15 | 0 | Hydrophobic |
| OAB | OH | TYR- 68 | 3.09 | 122.1 | H-Bond (Protein Donor) |
| CAR | CB | ALA- 69 | 4.1 | 0 | Hydrophobic |
| CAP | CB | ALA- 69 | 4.16 | 0 | Hydrophobic |
| CAR | CG | MET- 86 | 4.48 | 0 | Hydrophobic |
| CAS | CB | VAL- 90 | 3.74 | 0 | Hydrophobic |
| CAQ | CG2 | VAL- 90 | 3.57 | 0 | Hydrophobic |
| CAK | CG | GLU- 96 | 3.9 | 0 | Hydrophobic |
| CAQ | CG2 | ILE- 141 | 4 | 0 | Hydrophobic |
| CAO | CG2 | ILE- 141 | 4.23 | 0 | Hydrophobic |
| CAS | CB | ALA- 143 | 4.36 | 0 | Hydrophobic |
| CAH | CB | ALA- 143 | 4.32 | 0 | Hydrophobic |
| CAI | CB | ASN- 144 | 4.04 | 0 | Hydrophobic |
