sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2012-06-20
| 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 | 100 % |
| B-Factor: | 44.798 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.760 | 995.625 |
| % Hydrophobic | % Polar |
|---|---|
| 37.29 | 62.71 |
| According to VolSite | |
| HET Code: | C2F |
|---|---|
| Formula: | C20H23N7O6 |
| Molecular weight: | 457.440 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.29 % |
| Polar Surface area: | 204.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 53.351 | -1.33476 | -7.62342 |
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 | CB | HIS- 51 | 3.59 | 0 | Hydrophobic |
| C15 | CB | ILE- 79 | 3.8 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 79 | 3.87 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 79 | 4.06 | 0 | Hydrophobic |
| C14 | CB | ILE- 79 | 3.8 | 0 | Hydrophobic |
| C6 | CZ2 | TRP- 80 | 3.95 | 0 | Hydrophobic |
| C7 | CZ3 | TRP- 80 | 3.8 | 0 | Hydrophobic |
| C9 | CE2 | TRP- 80 | 3.85 | 0 | Hydrophobic |
| C7 | CE2 | TRP- 83 | 3.86 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 143 | 3.51 | 0 | Hydrophobic |
| NA2 | OD2 | ASP- 169 | 3.3 | 135.19 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 169 | 2.9 | 151.95 | H-Bond (Ligand Donor) |
| CB | CZ | PHE- 176 | 3.75 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 261 | 4.32 | 0 | Hydrophobic |
