sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2001-08-27
| Name: | Thymidylate synthase |
|---|---|
| ID: | TYSY_ECOLI |
| AC: | P0A884 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 43.043 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.305 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 54.50 | 45.50 |
| According to VolSite | |
| HET Code: | LYD |
|---|---|
| Formula: | C20H22N5O4 |
| Molecular weight: | 396.420 g/mol |
| DrugBank ID: | DB08131 |
| Buried Surface Area: | 52.37 % |
| Polar Surface area: | 152.5 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 46.697 | 40.2659 | 22.5227 |
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 |
| CG1 | CG2 | ILE- 79 | 4.45 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 79 | 4.2 | 0 | Hydrophobic |
| C3' | CB | ILE- 79 | 3.7 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 79 | 4.2 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 80 | 4.21 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 169 | 3.38 | 162.11 | H-Bond (Ligand Donor) |
| C5' | CB | PHE- 176 | 4.06 | 0 | Hydrophobic |
| C8 | CD1 | PHE- 176 | 4.48 | 0 | Hydrophobic |
