sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.890 Å
X-ray
2001-08-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.470 | 7.680 | 7.680 | 1.210 | 8.890 | 2 |
| Name: | Thymidylate synthase |
|---|---|
| ID: | TYSY_HUMAN |
| AC: | P04818 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.45 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 3 % |
| D | 97 % |
| B-Factor: | 21.572 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.134 | 648.000 |
| % Hydrophobic | % Polar |
|---|---|
| 51.56 | 48.44 |
| According to VolSite | |
| HET Code: | LYA |
|---|---|
| Formula: | C20H19N5O6 |
| Molecular weight: | 425.395 g/mol |
| DrugBank ID: | DB00642 |
| Buried Surface Area: | 58.06 % |
| Polar Surface area: | 192.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 44.2875 | 62.7251 | 54.821 |
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 |
| O31 | NZ | LYS- 77 | 3.83 | 0 | Ionic (Protein Cationic) |
| C25 | CD1 | PHE- 80 | 4.17 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 108 | 3.96 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 108 | 4.02 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 108 | 4.48 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 108 | 3.58 | 0 | Hydrophobic |
| C6 | CB | ILE- 108 | 3.51 | 0 | Hydrophobic |
| C7 | CE2 | TRP- 109 | 4.01 | 0 | Hydrophobic |
| C8 | CZ2 | TRP- 109 | 4.16 | 0 | Hydrophobic |
| N11 | OD1 | ASN- 112 | 3.24 | 136.52 | H-Bond (Ligand Donor) |
| N16 | OD1 | ASP- 218 | 3.12 | 162.17 | H-Bond (Ligand Donor) |
| C6 | SD | MET- 311 | 3.94 | 0 | Hydrophobic |
| N19 | O | ALA- 312 | 2.94 | 138.99 | H-Bond (Ligand Donor) |
| C8 | C5 | UMP- 314 | 3.62 | 0 | Hydrophobic |
| N18 | O | HOH- 447 | 3.48 | 141.2 | H-Bond (Protein Donor) |
