sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2012-04-05
| Name: | Bifunctional dihydrofolate reductase-thymidylate synthase |
|---|---|
| ID: | DRTS_TOXGO |
| AC: | Q07422 |
| Organism: | Toxoplasma gondii |
| Reign: | Eukaryota |
| TaxID: | 5811 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 97 % |
| F | 3 % |
| B-Factor: | 43.990 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.316 | 685.125 |
| % Hydrophobic | % Polar |
|---|---|
| 57.14 | 42.86 |
| According to VolSite | |
| HET Code: | CB3 |
|---|---|
| Formula: | C24H21N5O6 |
| Molecular weight: | 475.453 g/mol |
| DrugBank ID: | DB03541 |
| Buried Surface Area: | 63.04 % |
| Polar Surface area: | 180.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -7.55566 | -87.7531 | 35.1437 |
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 |
| CG | CD2 | PHE- 374 | 3.93 | 0 | Hydrophobic |
| C9 | CB | ILE- 402 | 4.28 | 0 | Hydrophobic |
| CP1 | CD1 | ILE- 402 | 4.18 | 0 | Hydrophobic |
| C15 | CB | ILE- 402 | 3.36 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 402 | 3.54 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 403 | 3.9 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 486 | 4.39 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 513 | 2.74 | 165.27 | H-Bond (Ligand Donor) |
| C16 | CD2 | LEU- 516 | 4.4 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 516 | 3.83 | 0 | Hydrophobic |
| C13 | CB | PHE- 520 | 4.38 | 0 | Hydrophobic |
| CP2 | CD1 | PHE- 520 | 3.44 | 0 | Hydrophobic |
| O2 | CZ | ARG- 603 | 3.83 | 0 | Ionic (Protein Cationic) |
| C4A | CG | MET- 608 | 4.19 | 0 | Hydrophobic |
| C8 | SD | MET- 608 | 3.62 | 0 | Hydrophobic |
| C16 | CE | MET- 608 | 3.77 | 0 | Hydrophobic |
| NA2 | O | ALA- 609 | 2.82 | 136.4 | H-Bond (Ligand Donor) |
| C4A | C1' | UMP- 701 | 3.7 | 0 | Hydrophobic |
| NA2 | O | HOH- 1006 | 3.28 | 121.17 | H-Bond (Ligand Donor) |
