sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-06-30
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 20.028 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.177 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.38 | 41.62 |
| According to VolSite | |
| HET Code: | D16 |
|---|---|
| Formula: | C21H20N4O6S |
| Molecular weight: | 456.472 g/mol |
| DrugBank ID: | DB00293 |
| Buried Surface Area: | 63.42 % |
| Polar Surface area: | 182.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 57.7972 | 8.17909 | -66.1591 |
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 |
| CM2 | CD2 | PHE- 14 | 4.5 | 0 | Hydrophobic |
| C8 | CB | PHE- 14 | 4.39 | 0 | Hydrophobic |
| CM2 | CB | ALA- 16 | 4.11 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 29 | 4.25 | 0 | Hydrophobic |
| OE1 | NE2 | HIS- 33 | 3.06 | 131.87 | H-Bond (Protein Donor) |
| N3 | OD2 | ASP- 37 | 2.7 | 176.09 | H-Bond (Ligand Donor) |
| CB | CG | PHE- 38 | 3.91 | 0 | Hydrophobic |
| CM2 | CD2 | PHE- 40 | 4.03 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 41 | 4.4 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 41 | 3.92 | 0 | Hydrophobic |
| C4A | CD2 | LEU- 41 | 3.98 | 0 | Hydrophobic |
| CP1 | CD2 | PHE- 65 | 3.98 | 0 | Hydrophobic |
| C9 | CG2 | THR- 69 | 3.87 | 0 | Hydrophobic |
| CP1 | CG2 | THR- 69 | 3.88 | 0 | Hydrophobic |
| S13 | CG1 | ILE- 73 | 3.76 | 0 | Hydrophobic |
| CP1 | CD1 | ILE- 73 | 4.2 | 0 | Hydrophobic |
| O2 | OG | SER- 77 | 3.5 | 135.85 | H-Bond (Protein Donor) |
| CP1 | CB | LEU- 123 | 3.52 | 0 | Hydrophobic |
| C7 | CB | LEU- 123 | 3.9 | 0 | Hydrophobic |
| CM2 | CB | THR- 144 | 4.17 | 0 | Hydrophobic |
| C9 | C5N | NAP- 515 | 3.48 | 0 | Hydrophobic |
| O4 | O | HOH- 565 | 2.8 | 149.93 | H-Bond (Protein Donor) |
