sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2011-11-12
| Name: | Bifunctional dihydrofolate reductase-thymidylate synthase |
|---|---|
| ID: | A7UD81_PLAFA |
| AC: | A7UD81 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 5833 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.028 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.506 | 668.250 |
| % Hydrophobic | % Polar |
|---|---|
| 65.66 | 34.34 |
| According to VolSite | |
| HET Code: | 1CY |
|---|---|
| Formula: | C11H16ClN5 |
| Molecular weight: | 253.731 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.39 % |
| Polar Surface area: | 83.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 0 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 28.0092 | 5.13994 | 59.088 |
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 |
| N8 | O | ILE- 14 | 2.97 | 158.31 | H-Bond (Ligand Donor) |
| N7 | O | CYS- 15 | 2.98 | 123.5 | H-Bond (Ligand Donor) |
| C9 | CG1 | VAL- 16 | 3.6 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 46 | 3.79 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 54 | 2.7 | 145.56 | H-Bond (Protein Donor) |
| N7 | OD1 | ASP- 54 | 2.98 | 167.28 | H-Bond (Ligand Donor) |
| C10 | SD | MET- 55 | 3.76 | 0 | Hydrophobic |
| C10 | CG | PHE- 58 | 3.59 | 0 | Hydrophobic |
| CL17 | CG2 | THR- 108 | 3.43 | 0 | Hydrophobic |
| C13 | CG2 | THR- 108 | 3.77 | 0 | Hydrophobic |
| CL17 | CG1 | ILE- 112 | 3.26 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 119 | 4.28 | 0 | Hydrophobic |
| N8 | O | ILE- 164 | 3.11 | 132.38 | H-Bond (Ligand Donor) |
| C14 | CD1 | ILE- 164 | 4.13 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 164 | 3.62 | 0 | Hydrophobic |
