sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
1997-09-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.220 | 7.610 | 7.610 | 0.390 | 8.000 | 2 |
| 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: | 15.205 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.028 | 567.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.60 | 49.40 |
| According to VolSite | |
| HET Code: | CB3 |
|---|---|
| Formula: | C24H21N5O6 |
| Molecular weight: | 475.453 g/mol |
| DrugBank ID: | DB03541 |
| Buried Surface Area: | 50.03 % |
| Polar Surface area: | 180.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 18.3506 | 45.9294 | -46.2806 |
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 |
| OE1 | NZ | LYS- 50 | 3.48 | 161.03 | H-Bond (Protein Donor) |
| OE1 | NZ | LYS- 50 | 3.48 | 0 | Ionic (Protein Cationic) |
| CG | CG | PRO- 53 | 4.16 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 81 | 4.39 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 81 | 3.48 | 0 | Hydrophobic |
| C16 | CG1 | ILE- 81 | 3.82 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 195 | 3.83 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 221 | 3.02 | 154.72 | H-Bond (Ligand Donor) |
| CB | CD2 | LEU- 224 | 4.38 | 0 | Hydrophobic |
| C13 | CB | PHE- 228 | 4.24 | 0 | Hydrophobic |
| CB | CZ | PHE- 228 | 4.48 | 0 | Hydrophobic |
| CG | CE1 | PHE- 228 | 3.29 | 0 | Hydrophobic |
| C12 | CZ | PHE- 228 | 3.46 | 0 | Hydrophobic |
| CP2 | CB | PHE- 228 | 3.51 | 0 | Hydrophobic |
| NA2 | OXT | VAL- 316 | 3.46 | 162.05 | H-Bond (Ligand Donor) |
| C4A | C1' | UMP- 317 | 3.51 | 0 | Hydrophobic |
| C8 | C1' | UMP- 317 | 3.87 | 0 | Hydrophobic |
