sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2001-01-08
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 20.634 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.335 | 718.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.75 | 42.25 |
| According to VolSite | |
| HET Code: | D16 |
|---|---|
| Formula: | C21H20N4O6S |
| Molecular weight: | 456.472 g/mol |
| DrugBank ID: | DB00293 |
| Buried Surface Area: | 56.36 % |
| 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 |
|---|---|---|
| 0.401375 | 12.3919 | 17.7663 |
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 |
| CB | CD2 | PHE- 80 | 4.23 | 0 | Hydrophobic |
| S13 | CB | ILE- 108 | 3.6 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 109 | 3.42 | 0 | Hydrophobic |
| CP1 | CZ2 | TRP- 109 | 3.53 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 192 | 4.2 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 218 | 2.63 | 154.19 | H-Bond (Ligand Donor) |
| CM2 | CE1 | TYR- 258 | 3.7 | 0 | Hydrophobic |
| CM2 | SD | MET- 311 | 4.34 | 0 | Hydrophobic |
| C4A | SD | MET- 311 | 3.95 | 0 | Hydrophobic |
| C8 | CE | MET- 311 | 3.61 | 0 | Hydrophobic |
| CM2 | CB | ALA- 312 | 3.66 | 0 | Hydrophobic |
| CM2 | C4' | UMP- 314 | 3.82 | 0 | Hydrophobic |
| O1 | O | HOH- 435 | 2.9 | 179.98 | H-Bond (Protein Donor) |
| O2 | O | HOH- 477 | 2.57 | 150.69 | H-Bond (Protein Donor) |
