sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2012-06-21
| Name: | Thymidylate synthase ThyA |
|---|---|
| ID: | TYSY_MYCTU |
| AC: | P9WFR9 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 97 % |
| D | 3 % |
| B-Factor: | 66.230 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.915 | 806.625 |
| % Hydrophobic | % Polar |
|---|---|
| 45.61 | 54.39 |
| According to VolSite | |
| HET Code: | D16 |
|---|---|
| Formula: | C21H20N4O6S |
| Molecular weight: | 456.472 g/mol |
| DrugBank ID: | DB00293 |
| Buried Surface Area: | 54.3 % |
| 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 |
|---|---|---|
| 2.25663 | -24.2846 | -9.77303 |
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 |
| CM2 | CG2 | THR- 22 | 4.32 | 0 | Hydrophobic |
| CG | CB | HIS- 51 | 4.25 | 0 | Hydrophobic |
| S13 | CB | ILE- 79 | 4.08 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 80 | 3.25 | 0 | Hydrophobic |
| CP1 | CZ2 | TRP- 80 | 3.88 | 0 | Hydrophobic |
| C8 | CE2 | TRP- 83 | 3.43 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 143 | 3.71 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 169 | 2.72 | 155.43 | H-Bond (Ligand Donor) |
| CM2 | CE2 | TYR- 209 | 3.48 | 0 | Hydrophobic |
| CM2 | C4' | UMP- 302 | 3.82 | 0 | Hydrophobic |
| C4A | C1' | UMP- 302 | 4.03 | 0 | Hydrophobic |
