sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2015-01-22
| Name: | Thymidylate synthase |
|---|---|
| ID: | TYSY_VZVO |
| AC: | Q4JQW2 |
| Organism: | Varicella-zoster virus |
| Reign: | Viruses |
| TaxID: | 341980 |
| EC Number: | 2.1.1.45 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 88 % |
| B | 12 % |
| B-Factor: | 42.702 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.361 | 661.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.41 | 54.59 |
| According to VolSite | |
| HET Code: | UMP |
|---|---|
| Formula: | C9H11N2O8P |
| Molecular weight: | 306.166 g/mol |
| DrugBank ID: | DB03800 |
| Buried Surface Area: | 69.63 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 3.827 | 72.7604 | -40.5995 |
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 |
| OP1 | NH2 | ARG- 38 | 3 | 120.46 | H-Bond (Protein Donor) |
| OP1 | CZ | ARG- 38 | 3.02 | 0 | Ionic (Protein Cationic) |
| OP2 | CZ | ARG- 163 | 3.13 | 0 | Ionic (Protein Cationic) |
| OP1 | CZ | ARG- 164 | 3.47 | 0 | Ionic (Protein Cationic) |
| C1' | SG | CYS- 183 | 4.31 | 0 | Hydrophobic |
| C5' | SG | CYS- 183 | 3.77 | 0 | Hydrophobic |
| OP3 | CZ | ARG- 203 | 3.24 | 0 | Ionic (Protein Cationic) |
| OP3 | NH2 | ARG- 203 | 2.77 | 136.57 | H-Bond (Protein Donor) |
| OP3 | NH1 | ARG- 203 | 2.94 | 130.5 | H-Bond (Protein Donor) |
| O2 | N | ASP- 206 | 2.69 | 149.32 | H-Bond (Protein Donor) |
| O3' | NE2 | HIS- 244 | 3.49 | 152.15 | H-Bond (Protein Donor) |
