sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2008-06-13
| Name: | Bifunctional dihydrofolate reductase-thymidylate synthase |
|---|---|
| ID: | DRTS_PLAFK |
| AC: | P13922 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 5839 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 60.785 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.375 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 62.90 | 37.10 |
| According to VolSite | |
| HET Code: | RJ1 |
|---|---|
| Formula: | C9H11ClF3N5 |
| Molecular weight: | 281.665 g/mol |
| DrugBank ID: | DB08478 |
| Buried Surface Area: | 62.16 % |
| Polar Surface area: | 101.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 5 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 31.2093 | -29.7163 | 7.13278 |
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 |
| C15 | OD2 | ASP- 54 | 3.63 | 0 | Ionic (Ligand Cationic) |
| C15 | OD1 | ASP- 54 | 3.81 | 0 | Ionic (Ligand Cationic) |
| N16 | OD1 | ASP- 54 | 3.37 | 141.32 | H-Bond (Ligand Donor) |
| N18 | OD2 | ASP- 54 | 2.56 | 132.77 | H-Bond (Ligand Donor) |
| N18 | OD1 | ASP- 54 | 3.39 | 141.95 | H-Bond (Ligand Donor) |
| F9 | CG | MET- 55 | 4.47 | 0 | Hydrophobic |
| C8 | SD | MET- 55 | 3.91 | 0 | Hydrophobic |
| CL7 | CZ | PHE- 58 | 4.12 | 0 | Hydrophobic |
| C2 | CG1 | ILE- 112 | 4.26 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 112 | 4.4 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 119 | 4.49 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 119 | 4.49 | 0 | Hydrophobic |
| F10 | CD2 | LEU- 119 | 4.1 | 0 | Hydrophobic |
| CL7 | CG1 | ILE- 164 | 3.35 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 164 | 4.01 | 0 | Hydrophobic |
| CL7 | C5N | NDP- 610 | 3.44 | 0 | Hydrophobic |
