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
1995-12-05
| 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: | 15.559 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.568 | 1879.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.93 | 59.07 |
| According to VolSite | |
| HET Code: | UMP |
|---|---|
| Formula: | C9H11N2O8P |
| Molecular weight: | 306.166 g/mol |
| DrugBank ID: | DB03800 |
| Buried Surface Area: | 59.86 % |
| 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 |
|---|---|---|
| 14.8817 | 49.4407 | -55.6471 |
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 |
| OP1 | CZ | ARG- 23 | 3.28 | 0 | Ionic (Protein Cationic) |
| OP2 | CZ | ARG- 23 | 3.57 | 0 | Ionic (Protein Cationic) |
| OP2 | NE | ARG- 23 | 3.1 | 121.07 | H-Bond (Protein Donor) |
| C5' | CD1 | LEU- 195 | 4.21 | 0 | Hydrophobic |
| C5' | SG | CYS- 198 | 4.2 | 0 | Hydrophobic |
| C2' | SG | CYS- 198 | 3.6 | 0 | Hydrophobic |
| OP1 | CZ | ARG- 218 | 3.58 | 0 | Ionic (Protein Cationic) |
| OP3 | CZ | ARG- 218 | 3.42 | 0 | Ionic (Protein Cationic) |
| OP1 | NH1 | ARG- 218 | 3.47 | 131.18 | H-Bond (Protein Donor) |
| OP1 | NH2 | ARG- 218 | 2.82 | 166.11 | H-Bond (Protein Donor) |
| OP3 | NH1 | ARG- 218 | 2.79 | 120.34 | H-Bond (Protein Donor) |
| OP3 | OG | SER- 219 | 3.06 | 128.83 | H-Bond (Protein Donor) |
| C2' | CB | SER- 219 | 4.02 | 0 | Hydrophobic |
| O2 | N | ASP- 221 | 2.75 | 163.42 | H-Bond (Protein Donor) |
| C1' | CB | ASP- 221 | 4.14 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 229 | 2.88 | 157.14 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 229 | 2.75 | 172.71 | H-Bond (Protein Donor) |
| O3' | NE2 | HIS- 259 | 2.62 | 167.33 | H-Bond (Ligand Donor) |
