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
1996-01-23
| Name: | Thymidylate synthase |
|---|---|
| ID: | TYSY_LACCA |
| AC: | P00469 |
| Organism: | Lactobacillus casei |
| Reign: | Bacteria |
| TaxID: | 1582 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.309 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.860 | 1647.000 |
| % Hydrophobic | % Polar |
|---|---|
| 40.57 | 59.43 |
| According to VolSite | |
| HET Code: | DCM |
|---|---|
| Formula: | C9H12N3O7P |
| Molecular weight: | 305.181 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.6 % |
| Polar Surface area: | 170.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| 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 |
|---|---|---|
| 15.1929 | 49.5466 | -55.6272 |
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 |
| O1P | CZ | ARG- 23 | 2.93 | 0 | Ionic (Protein Cationic) |
| C5' | CD1 | LEU- 195 | 4.14 | 0 | Hydrophobic |
| C1' | SG | CYS- 198 | 4.24 | 0 | Hydrophobic |
| C5' | SG | CYS- 198 | 3.46 | 0 | Hydrophobic |
| O5' | NH1 | ARG- 218 | 3.47 | 124.17 | H-Bond (Protein Donor) |
| O2P | NH1 | ARG- 218 | 3.07 | 166.58 | H-Bond (Protein Donor) |
| O3P | NH2 | ARG- 218 | 3.07 | 168.29 | H-Bond (Protein Donor) |
| O3P | CZ | ARG- 218 | 3.8 | 0 | Ionic (Protein Cationic) |
| C5' | CB | SER- 219 | 3.74 | 0 | Hydrophobic |
| C2' | CB | SER- 219 | 4.26 | 0 | Hydrophobic |
| O5' | OG | SER- 219 | 2.99 | 148.71 | H-Bond (Protein Donor) |
| O2 | N | ASP- 221 | 2.7 | 151.44 | H-Bond (Protein Donor) |
| C1' | CB | ASP- 221 | 4.15 | 0 | Hydrophobic |
| N3 | ND2 | ASN- 229 | 3.32 | 145.78 | H-Bond (Protein Donor) |
| N4 | OD1 | ASN- 229 | 3.09 | 144.95 | H-Bond (Ligand Donor) |
| O3' | NE2 | HIS- 259 | 3.08 | 138.16 | H-Bond (Ligand Donor) |
| O3' | OH | TYR- 261 | 3.07 | 163.35 | H-Bond (Protein Donor) |
