sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 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: | 30.147 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.427 | 661.500 |
| % Hydrophobic | % Polar |
|---|---|
| 62.24 | 37.76 |
| According to VolSite | |
| HET Code: | CP6 |
|---|---|
| Formula: | C12H13ClN4 |
| Molecular weight: | 248.711 g/mol |
| DrugBank ID: | DB00205 |
| Buried Surface Area: | 69.71 % |
| Polar Surface area: | 77.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 28.035 | 5.41082 | 58.9211 |
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 |
| N13 | O | ILE- 14 | 2.85 | 164.51 | H-Bond (Ligand Donor) |
| C4 | CG1 | VAL- 16 | 4.27 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 16 | 4.39 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 46 | 4.22 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 54 | 3.41 | 135.4 | H-Bond (Ligand Donor) |
| N6 | OD2 | ASP- 54 | 2.55 | 150.03 | H-Bond (Ligand Donor) |
| N14 | OD1 | ASP- 54 | 2.95 | 159.75 | H-Bond (Ligand Donor) |
| C16 | CG | MET- 55 | 4.2 | 0 | Hydrophobic |
| C15 | CG | PHE- 58 | 4.49 | 0 | Hydrophobic |
| C16 | CB | PHE- 58 | 3.84 | 0 | Hydrophobic |
| C12 | CZ | PHE- 58 | 3.48 | 0 | Hydrophobic |
| CL1 | CG2 | THR- 108 | 3.4 | 0 | Hydrophobic |
| CL1 | CG1 | ILE- 112 | 3.45 | 0 | Hydrophobic |
| N13 | O | ILE- 164 | 2.91 | 131.25 | H-Bond (Ligand Donor) |
| C11 | CD1 | ILE- 164 | 4.09 | 0 | Hydrophobic |
| N14 | O | HOH- 1003 | 3.34 | 129.44 | H-Bond (Ligand Donor) |
