sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.330 Å
X-ray
2003-02-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.960 | 8.960 | 8.960 | 0.000 | 8.960 | 1 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 37.971 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.555 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 67.40 | 32.60 |
| According to VolSite | |
| HET Code: | WRA |
|---|---|
| Formula: | C14H20Cl3N5O2 |
| Molecular weight: | 396.700 g/mol |
| DrugBank ID: | DB08734 |
| Buried Surface Area: | 65.63 % |
| 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 |
|---|---|---|
| 28.0213 | 6.08146 | 59.7873 |
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 | ILE- 14 | 2.98 | 170.77 | H-Bond (Ligand Donor) |
| CM2 | CB | ALA- 16 | 4.01 | 0 | Hydrophobic |
| CM2 | CD2 | LEU- 46 | 4.05 | 0 | Hydrophobic |
| CL3 | CD1 | LEU- 46 | 4.04 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 54 | 2.74 | 146.64 | H-Bond (Protein Donor) |
| NH1 | OD1 | ASP- 54 | 2.83 | 157.92 | H-Bond (Ligand Donor) |
| CM1 | CE | MET- 55 | 3.81 | 0 | Hydrophobic |
| CL2 | CE | MET- 55 | 4.2 | 0 | Hydrophobic |
| C13 | SD | MET- 55 | 3.82 | 0 | Hydrophobic |
| C14 | CE | MET- 55 | 3.56 | 0 | Hydrophobic |
| C8 | CZ | PHE- 58 | 3.63 | 0 | Hydrophobic |
| CM1 | CG | PHE- 58 | 4.01 | 0 | Hydrophobic |
| CL1 | CE2 | PHE- 58 | 3.77 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 112 | 4.04 | 0 | Hydrophobic |
| C12 | CG1 | ILE- 112 | 3.87 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 112 | 4.14 | 0 | Hydrophobic |
| CL2 | CG | PRO- 113 | 3.77 | 0 | Hydrophobic |
| CL2 | CE2 | PHE- 116 | 3.7 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 119 | 3.43 | 0 | Hydrophobic |
| C8 | CB | ILE- 164 | 3.97 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 164 | 4.29 | 0 | Hydrophobic |
| NH2 | O | ILE- 164 | 3 | 134.71 | H-Bond (Ligand Donor) |
| C8 | C4N | NDP- 610 | 4.08 | 0 | Hydrophobic |
| CM2 | C3N | NDP- 610 | 4.17 | 0 | Hydrophobic |
| C9 | C5N | NDP- 610 | 3.54 | 0 | Hydrophobic |
