sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2001-06-22
| 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 |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 29.449 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.140 | 793.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.51 | 51.49 |
| According to VolSite | |
| HET Code: | DDT |
|---|---|
| Formula: | C33H32N3O7S2 |
| Molecular weight: | 646.753 g/mol |
| DrugBank ID: | DB03157 |
| Buried Surface Area: | 48.81 % |
| Polar Surface area: | 152.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 14.782 | 39.0441 | 30.0742 |
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 |
| C6 | CB | SER- 54 | 3.92 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 55 | 3.7 | 0 | Hydrophobic |
| C10 | CG2 | ILE- 79 | 4.45 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 79 | 3.58 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 79 | 4.02 | 0 | Hydrophobic |
| C4A | CG1 | ILE- 79 | 3.52 | 0 | Hydrophobic |
| C9' | CZ2 | TRP- 83 | 3.93 | 0 | Hydrophobic |
| C2' | CD1 | LEU- 143 | 4.43 | 0 | Hydrophobic |
| C9' | CD2 | LEU- 143 | 4.19 | 0 | Hydrophobic |
| C6' | CB | ASP- 169 | 3.94 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 172 | 4.29 | 0 | Hydrophobic |
| C16 | CG | LEU- 172 | 3.74 | 0 | Hydrophobic |
| C9 | CB | PHE- 176 | 3.75 | 0 | Hydrophobic |
| C8 | CB | PHE- 176 | 3.97 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 262 | 3.65 | 0 | Hydrophobic |
| C7' | CG2 | VAL- 262 | 4.04 | 0 | Hydrophobic |
| C7' | CB | ALA- 263 | 4.15 | 0 | Hydrophobic |
| C2' | C5' | UMP- 303 | 4.41 | 0 | Hydrophobic |
| C9' | C5' | UMP- 303 | 4.41 | 0 | Hydrophobic |
| C8X | C4' | UMP- 303 | 3.53 | 0 | Hydrophobic |
| C8' | C4' | UMP- 303 | 3.51 | 0 | Hydrophobic |
| C5' | C1' | UMP- 303 | 3.74 | 0 | Hydrophobic |
| O2 | O | HOH- 549 | 2.57 | 179.97 | H-Bond (Protein Donor) |
