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
2009-11-03
| Name: | Bifunctional dihydrofolate reductase-thymidylate synthase |
|---|---|
| ID: | Q8T5T8_TRYCR |
| AC: | Q8T5T8 |
| Organism: | Trypanosoma cruzi |
| Reign: | Eukaryota |
| TaxID: | 5693 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 40.397 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.607 | 597.375 |
| % Hydrophobic | % Polar |
|---|---|
| 68.93 | 31.07 |
| According to VolSite | |
| HET Code: | DQ1 |
|---|---|
| Formula: | C22H27N5O4 |
| Molecular weight: | 425.481 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.31 % |
| Polar Surface area: | 134.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 66.8427 | -34.124 | 24.1939 |
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 |
| N2 | O | VAL- 26 | 2.81 | 166.9 | H-Bond (Ligand Donor) |
| N3 | O | VAL- 27 | 3.44 | 123.42 | H-Bond (Ligand Donor) |
| C3 | CD1 | ILE- 41 | 4 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 41 | 3.65 | 0 | Hydrophobic |
| C10 | CB | VAL- 45 | 4.42 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 48 | 2.81 | 171.89 | H-Bond (Ligand Donor) |
| N5 | OD2 | ASP- 48 | 2.95 | 159.63 | H-Bond (Ligand Donor) |
| C5 | CE | MET- 49 | 3.86 | 0 | Hydrophobic |
| C8 | CE | MET- 49 | 3.6 | 0 | Hydrophobic |
| C11 | SD | MET- 49 | 3.6 | 0 | Hydrophobic |
| C21 | SD | MET- 49 | 3.74 | 0 | Hydrophobic |
| C16 | CE | MET- 49 | 3.5 | 0 | Hydrophobic |
| C4 | CG2 | THR- 80 | 3.97 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 84 | 4.13 | 0 | Hydrophobic |
| C13 | CG1 | ILE- 84 | 3.8 | 0 | Hydrophobic |
| C6 | CG | PRO- 85 | 4.42 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 91 | 4.48 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 91 | 3.88 | 0 | Hydrophobic |
| N2 | O | ILE- 154 | 3.11 | 140.58 | H-Bond (Ligand Donor) |
| C4 | C5N | NAP- 702 | 4.2 | 0 | Hydrophobic |
