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
1995-06-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.810 | 4.940 | 4.940 | 0.120 | 5.060 | 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: | 4.341 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.078 | 1420.875 |
| % Hydrophobic | % Polar |
|---|---|
| 41.33 | 58.67 |
| According to VolSite | |
| HET Code: | TMP |
|---|---|
| Formula: | C10H13N2O8P |
| Molecular weight: | 320.193 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 46.44 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| 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 |
|---|---|---|
| 15.255 | 47.7915 | -53.4765 |
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 |
| C5M | CH2 | TRP- 82 | 4.13 | 0 | Hydrophobic |
| C5M | CD2 | LEU- 195 | 3.37 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 195 | 4.12 | 0 | Hydrophobic |
| C1' | SG | CYS- 198 | 3.33 | 0 | Hydrophobic |
| O1P | CZ | ARG- 218 | 3.82 | 0 | Ionic (Protein Cationic) |
| O1P | NH2 | ARG- 218 | 3.13 | 165.71 | H-Bond (Protein Donor) |
| O2P | NH2 | ARG- 218 | 3.16 | 127.46 | H-Bond (Protein Donor) |
| O1P | OG | SER- 219 | 3.05 | 134.57 | H-Bond (Protein Donor) |
| O5' | OG | SER- 219 | 3.38 | 144.11 | H-Bond (Protein Donor) |
| C2' | CB | ASP- 221 | 3.9 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 229 | 3.23 | 149.5 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 229 | 3.5 | 153.02 | H-Bond (Protein Donor) |
| O3' | NE2 | HIS- 259 | 3.15 | 165.31 | H-Bond (Ligand Donor) |
