sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.590 Å
X-ray
2012-07-06
| Name: | Probable flavin-dependent thymidylate synthase |
|---|---|
| ID: | THYX_PBCV1 |
| AC: | O41156 |
| Organism: | Paramecium bursaria Chlorella virus 1 |
| Reign: | Viruses |
| TaxID: | 10506 |
| EC Number: | 2.1.1.148 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| M | 54 % |
| O | 42 % |
| P | 4 % |
| B-Factor: | 46.459 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.386 | 691.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.00 | 60.00 |
| According to VolSite | |
| HET Code: | 0VJ |
|---|---|
| Formula: | C18H13O4 |
| Molecular weight: | 293.293 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.99 % |
| Polar Surface area: | 66.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 38.7641 | 104.12 | -49.185 |
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 |
| C04 | CG | GLN- 75 | 4.37 | 0 | Hydrophobic |
| C03 | CG | ARG- 78 | 4.31 | 0 | Hydrophobic |
| C01 | CB | GLU- 86 | 3.76 | 0 | Hydrophobic |
| O02 | OG | SER- 88 | 3.36 | 163.66 | H-Bond (Protein Donor) |
| C17 | CB | GLN- 89 | 3.98 | 0 | Hydrophobic |
| C06 | CG | GLN- 89 | 3.99 | 0 | Hydrophobic |
| O02 | N | GLN- 89 | 3.07 | 157.3 | H-Bond (Protein Donor) |
| C | CD | ARG- 90 | 3.84 | 0 | Hydrophobic |
| C15 | CG | ARG- 90 | 3.38 | 0 | Hydrophobic |
| C15 | CG | GLU- 152 | 4.48 | 0 | Hydrophobic |
| C16 | CB | GLU- 152 | 4 | 0 | Hydrophobic |
| O03 | NH2 | ARG- 182 | 2.87 | 143.13 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 182 | 2.82 | 165.27 | H-Bond (Protein Donor) |
| C | CB | GLN- 188 | 4.32 | 0 | Hydrophobic |
| C16 | CB | GLN- 188 | 3.77 | 0 | Hydrophobic |
| C11 | C6 | FAD- 301 | 3.35 | 0 | Hydrophobic |
| C04 | C1' | FAD- 301 | 4 | 0 | Hydrophobic |
