sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2006-03-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.650 | 5.650 | 5.650 | 0.000 | 5.650 | 1 |
| 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: | 31.031 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.523 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 47.28 | 52.72 |
| According to VolSite | |
| HET Code: | UMP |
|---|---|
| Formula: | C9H11N2O8P |
| Molecular weight: | 306.166 g/mol |
| DrugBank ID: | DB03800 |
| Buried Surface Area: | 54.13 % |
| 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 |
|---|---|---|
| 15.0483 | 49.6117 | -55.8474 |
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 |
| O5' | NE | ARG- 23 | 2.93 | 142.66 | H-Bond (Protein Donor) |
| O5' | NH2 | ARG- 23 | 2.8 | 148.83 | H-Bond (Protein Donor) |
| OP1 | NE | ARG- 23 | 2.61 | 132.14 | H-Bond (Protein Donor) |
| OP1 | CZ | ARG- 23 | 3.83 | 0 | Ionic (Protein Cationic) |
| C5' | CD1 | LEU- 195 | 3.94 | 0 | Hydrophobic |
| C1' | SG | CYS- 198 | 4.1 | 0 | Hydrophobic |
| C5' | SG | CYS- 198 | 3.95 | 0 | Hydrophobic |
| OP2 | NH2 | ARG- 218 | 3.12 | 148.79 | H-Bond (Protein Donor) |
| OP3 | NH2 | ARG- 218 | 3.34 | 127.75 | H-Bond (Protein Donor) |
| OP3 | NH1 | ARG- 218 | 2.68 | 163.37 | H-Bond (Protein Donor) |
| OP2 | CZ | ARG- 218 | 3.88 | 0 | Ionic (Protein Cationic) |
| OP3 | CZ | ARG- 218 | 3.43 | 0 | Ionic (Protein Cationic) |
| OP2 | OG | SER- 219 | 2.73 | 167.22 | H-Bond (Protein Donor) |
| C2' | CB | ASP- 221 | 3.92 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 229 | 3.01 | 150.21 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 229 | 2.66 | 152.84 | H-Bond (Protein Donor) |
| O3' | NE2 | HIS- 259 | 2.78 | 160.37 | H-Bond (Protein Donor) |
