sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2011-01-24
| Name: | Bifunctional dihydrofolate reductase-thymidylate synthase |
|---|---|
| ID: | D9N170_PLAFA |
| AC: | D9N170 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 5833 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.073 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.403 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 58.91 | 41.09 |
| According to VolSite | |
| HET Code: | CP6 |
|---|---|
| Formula: | C12H13ClN4 |
| Molecular weight: | 248.711 g/mol |
| DrugBank ID: | DB00205 |
| Buried Surface Area: | 73.25 % |
| 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 |
|---|---|---|
| 28.2902 | 5.20065 | 58.8027 |
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 | 2.83 | 164.35 | H-Bond (Ligand Donor) |
| C15 | CD1 | LEU- 46 | 4.24 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 46 | 4.16 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 54 | 3.42 | 134.93 | H-Bond (Ligand Donor) |
| N6 | OD2 | ASP- 54 | 2.59 | 159.84 | H-Bond (Ligand Donor) |
| N14 | OD1 | ASP- 54 | 2.92 | 164.75 | H-Bond (Ligand Donor) |
| C16 | CG | MET- 55 | 3.68 | 0 | Hydrophobic |
| C16 | CB | PHE- 58 | 4.15 | 0 | Hydrophobic |
| C12 | CZ | PHE- 58 | 3.47 | 0 | Hydrophobic |
| CL1 | CB | ASN- 108 | 3.65 | 0 | Hydrophobic |
| CL1 | CG1 | ILE- 112 | 3.64 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 164 | 4.43 | 0 | Hydrophobic |
| N13 | O | LEU- 164 | 3.19 | 127.41 | H-Bond (Ligand Donor) |
| N14 | O | HOH- 1159 | 3.38 | 138.31 | H-Bond (Ligand Donor) |
