sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.740 Å
X-ray
2012-03-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.380 | 6.380 | 6.380 | 0.000 | 6.380 | 1 |
| Name: | Thymidylate synthase |
|---|---|
| ID: | TYSY_MOUSE |
| AC: | P07607 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 2.1.1.45 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 3 % |
| D | 97 % |
| B-Factor: | 39.526 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.180 | 904.500 |
| % Hydrophobic | % Polar |
|---|---|
| 52.24 | 47.76 |
| According to VolSite | |
| HET Code: | D16 |
|---|---|
| Formula: | C21H20N4O6S |
| Molecular weight: | 456.472 g/mol |
| DrugBank ID: | DB00293 |
| Buried Surface Area: | 52.39 % |
| Polar Surface area: | 182.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -14.4067 | -9.30625 | 32.3528 |
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 |
| S13 | CG2 | ILE- 102 | 4.44 | 0 | Hydrophobic |
| C9 | CH2 | TRP- 103 | 3.89 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 212 | 2.56 | 168.49 | H-Bond (Ligand Donor) |
| C4A | CD2 | LEU- 215 | 4.08 | 0 | Hydrophobic |
| CG | CD1 | LEU- 215 | 3.55 | 0 | Hydrophobic |
| S13 | CB | PHE- 219 | 4.04 | 0 | Hydrophobic |
| CP1 | CD1 | PHE- 219 | 3.57 | 0 | Hydrophobic |
| S13 | CD2 | PHE- 219 | 3.48 | 0 | Hydrophobic |
| CM2 | CE2 | TYR- 252 | 3.26 | 0 | Hydrophobic |
| OE1 | N | MET- 303 | 3.35 | 167.72 | H-Bond (Protein Donor) |
| CM2 | C4' | UMP- 401 | 4.04 | 0 | Hydrophobic |
| C4A | C1' | UMP- 401 | 3.99 | 0 | Hydrophobic |
| OE2 | O | HOH- 699 | 2.78 | 141.12 | H-Bond (Protein Donor) |
