sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
1997-06-30
| 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 | 100 % |
| B-Factor: | 22.292 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.651 | 1090.125 |
| % Hydrophobic | % Polar |
|---|---|
| 30.34 | 69.66 |
| According to VolSite | |
| HET Code: | DDU |
|---|---|
| Formula: | C9H12N2O4 |
| Molecular weight: | 212.203 g/mol |
| DrugBank ID: | DB03274 |
| Buried Surface Area: | 51.26 % |
| Polar Surface area: | 78.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -28.4613 | -9.35173 | 20.4585 |
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 |
| C2' | SG | CYS- 146 | 4.16 | 0 | Hydrophobic |
| C2' | CB | SER- 167 | 4 | 0 | Hydrophobic |
| O2 | N | ASP- 169 | 2.91 | 161.47 | H-Bond (Protein Donor) |
| C1' | CB | ASP- 169 | 4 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 177 | 3 | 175.75 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 177 | 2.65 | 125.11 | H-Bond (Protein Donor) |
