sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2011-04-08
| Name: | Bifunctional dihydrofolate reductase-thymidylate synthase |
|---|---|
| ID: | DRTS_TRYBB |
| AC: | Q27783 |
| Organism: | Trypanosoma brucei brucei |
| Reign: | Eukaryota |
| TaxID: | 5702 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.762 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.577 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 66.00 | 34.00 |
| According to VolSite | |
| HET Code: | WRA |
|---|---|
| Formula: | C14H20Cl3N5O2 |
| Molecular weight: | 396.700 g/mol |
| DrugBank ID: | DB08734 |
| Buried Surface Area: | 69.07 % |
| Polar Surface area: | 101.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -19.111 | 21.9636 | 8.83367 |
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 |
| NH2 | O | VAL- 32 | 2.7 | 171.05 | H-Bond (Ligand Donor) |
| CM2 | CB | ALA- 34 | 3.91 | 0 | Hydrophobic |
| CL3 | CB | THR- 46 | 4.34 | 0 | Hydrophobic |
| CM2 | CD1 | ILE- 47 | 3.42 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 47 | 3.65 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 54 | 2.7 | 158.51 | H-Bond (Protein Donor) |
| NH1 | OD1 | ASP- 54 | 2.7 | 175.85 | H-Bond (Ligand Donor) |
| CM1 | SD | MET- 55 | 3.74 | 0 | Hydrophobic |
| CL1 | CE | MET- 55 | 3.46 | 0 | Hydrophobic |
| C14 | CE | MET- 55 | 3.31 | 0 | Hydrophobic |
| C8 | CZ | PHE- 58 | 3.47 | 0 | Hydrophobic |
| CM1 | CG | PHE- 58 | 3.9 | 0 | Hydrophobic |
| CL1 | CE1 | PHE- 58 | 4.3 | 0 | Hydrophobic |
| C9 | CG2 | THR- 86 | 3.52 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 90 | 4.27 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 90 | 3.63 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 90 | 3.46 | 0 | Hydrophobic |
| CL2 | CG | PRO- 91 | 3.42 | 0 | Hydrophobic |
| CL1 | CD2 | PHE- 94 | 3.55 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 97 | 3.82 | 0 | Hydrophobic |
| C8 | CB | ILE- 160 | 3.91 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 160 | 3.86 | 0 | Hydrophobic |
| NH2 | O | ILE- 160 | 3.2 | 141.58 | H-Bond (Ligand Donor) |
| C8 | C4N | NDP- 601 | 4.33 | 0 | Hydrophobic |
| CM2 | C3N | NDP- 601 | 4.32 | 0 | Hydrophobic |
| C9 | C5N | NDP- 601 | 4 | 0 | Hydrophobic |
