sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2009-09-30
| Name: | Bifunctional dihydrofolate reductase-thymidylate synthase |
|---|---|
| ID: | A7ASX7_BABBO |
| AC: | A7ASX7 |
| Organism: | Babesia bovis |
| Reign: | Eukaryota |
| TaxID: | 5865 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 2 % |
| B | 98 % |
| B-Factor: | 12.717 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 6 |
| Cofactors: | UMP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.142 | 550.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.69 | 50.31 |
| According to VolSite | |
| HET Code: | LYA |
|---|---|
| Formula: | C20H19N5O6 |
| Molecular weight: | 425.395 g/mol |
| DrugBank ID: | DB00642 |
| Buried Surface Area: | 62.68 % |
| Polar Surface area: | 192.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 27.4487 | -56.3738 | -24.6572 |
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 |
| C25 | CB | ALA- 278 | 3.83 | 0 | Hydrophobic |
| O28 | OG | SER- 281 | 2.78 | 166.86 | H-Bond (Protein Donor) |
| C7 | CD1 | ILE- 306 | 4.07 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 306 | 4.27 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 306 | 3.6 | 0 | Hydrophobic |
| C6 | CB | ILE- 306 | 3.52 | 0 | Hydrophobic |
| N11 | OD1 | ASN- 310 | 2.8 | 153.53 | H-Bond (Ligand Donor) |
| N16 | OD2 | ASP- 416 | 2.93 | 163.1 | H-Bond (Ligand Donor) |
| C4 | CD1 | LEU- 419 | 4.44 | 0 | Hydrophobic |
| C2 | CB | PHE- 423 | 4.25 | 0 | Hydrophobic |
| C25 | CZ | PHE- 423 | 4.01 | 0 | Hydrophobic |
| C5 | SD | MET- 509 | 3.63 | 0 | Hydrophobic |
| N19 | O | SER- 510 | 2.76 | 154.4 | H-Bond (Ligand Donor) |
| N18 | O | HOH- 524 | 2.57 | 146.49 | H-Bond (Protein Donor) |
| N19 | O | HOH- 529 | 3.31 | 126.11 | H-Bond (Ligand Donor) |
| O30 | O | HOH- 545 | 2.69 | 179.98 | H-Bond (Protein Donor) |
| O31 | O | HOH- 552 | 2.61 | 179.96 | H-Bond (Protein Donor) |
