sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2001-01-27
| Name: | Thymidylate synthase |
|---|---|
| ID: | TYSY_HUMAN |
| AC: | P04818 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.45 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 96 % |
| B | 4 % |
| B-Factor: | 44.238 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.830 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 53.49 | 46.51 |
| According to VolSite | |
| HET Code: | D16 |
|---|---|
| Formula: | C21H20N4O6S |
| Molecular weight: | 456.472 g/mol |
| DrugBank ID: | DB00293 |
| Buried Surface Area: | 41.77 % |
| Polar Surface area: | 182.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 34.5739 | 60.6614 | 51.5469 |
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 |
| CG | CD2 | PHE- 80 | 3.46 | 0 | Hydrophobic |
| C9 | CB | ILE- 108 | 4.36 | 0 | Hydrophobic |
| S13 | CB | ILE- 108 | 3.67 | 0 | Hydrophobic |
| CP1 | CD1 | ILE- 108 | 4.01 | 0 | Hydrophobic |
| S13 | CD2 | LEU- 221 | 4.06 | 0 | Hydrophobic |
| C4A | CD2 | LEU- 221 | 4.07 | 0 | Hydrophobic |
| O4 | N | GLY- 222 | 2.92 | 132.23 | H-Bond (Protein Donor) |
| CP1 | CD1 | PHE- 225 | 4.05 | 0 | Hydrophobic |
| CM2 | CE1 | TYR- 258 | 3.46 | 0 | Hydrophobic |
| CM2 | C4' | UMP- 314 | 4.19 | 0 | Hydrophobic |
| C4A | C1' | UMP- 314 | 3.79 | 0 | Hydrophobic |
