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: | 15.767 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.990 | 1009.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.81 | 57.19 |
| According to VolSite | |
| HET Code: | CB3 |
|---|---|
| Formula: | C24H21N5O6 |
| Molecular weight: | 475.453 g/mol |
| DrugBank ID: | DB03541 |
| Buried Surface Area: | 52.15 % |
| 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 |
|---|---|---|
| 19.5435 | 45.3961 | -46.9223 |
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 |
| C9 | CG2 | ILE- 81 | 3.98 | 0 | Hydrophobic |
| CP1 | CG2 | ILE- 81 | 3.54 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 81 | 3.75 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 195 | 3.86 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 221 | 2.84 | 141.78 | H-Bond (Ligand Donor) |
| CB | CB | LEU- 224 | 3.4 | 0 | Hydrophobic |
| CG | CD2 | LEU- 224 | 4.1 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 224 | 3.63 | 0 | Hydrophobic |
| CP2 | CD2 | PHE- 228 | 4.06 | 0 | Hydrophobic |
| CP3 | CB | PHE- 228 | 3.53 | 0 | Hydrophobic |
| NA2 | OH | TYR- 261 | 3.01 | 128.15 | H-Bond (Ligand Donor) |
| CG | CB | ALA- 312 | 4.21 | 0 | Hydrophobic |
| C4A | C1' | UMP- 317 | 3.98 | 0 | Hydrophobic |
| O1 | O | HOH- 351 | 2.92 | 132.13 | H-Bond (Protein Donor) |
