sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2011-02-03
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_CANAX |
| AC: | P22906 |
| Organism: | Candida albicans |
| Reign: | Eukaryota |
| TaxID: | 5476 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 32.206 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.312 | 891.000 |
| % Hydrophobic | % Polar |
|---|---|
| 57.95 | 42.05 |
| According to VolSite | |
| HET Code: | N22 |
|---|---|
| Formula: | C17H20N4O2 |
| Molecular weight: | 312.366 g/mol |
| DrugBank ID: | DB08234 |
| Buried Surface Area: | 55.09 % |
| Polar Surface area: | 96.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -10.1789 | 42.9907 | -18.5826 |
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 |
| N7 | O | ILE- 9 | 2.87 | 159.86 | H-Bond (Ligand Donor) |
| N8 | O | VAL- 10 | 3.3 | 133.45 | H-Bond (Ligand Donor) |
| C8 | SD | MET- 25 | 3.73 | 0 | Hydrophobic |
| C2 | CE | MET- 25 | 3.72 | 0 | Hydrophobic |
| C10 | CE | MET- 25 | 3.79 | 0 | Hydrophobic |
| C11 | CE | MET- 25 | 4.03 | 0 | Hydrophobic |
| N4 | OE1 | GLU- 32 | 2.69 | 158.02 | H-Bond (Ligand Donor) |
| N8 | OE2 | GLU- 32 | 2.69 | 171.16 | H-Bond (Ligand Donor) |
| N8 | OE1 | GLU- 32 | 3.27 | 130 | H-Bond (Ligand Donor) |
| C7 | CG | PHE- 36 | 3.9 | 0 | Hydrophobic |
| C10 | CZ | PHE- 36 | 4.08 | 0 | Hydrophobic |
| C4 | CD2 | PHE- 36 | 4.35 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 36 | 3.44 | 0 | Hydrophobic |
| C11 | CG2 | THR- 58 | 3.94 | 0 | Hydrophobic |
| C14 | CG2 | THR- 58 | 4.38 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 62 | 3.63 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 69 | 4.4 | 0 | Hydrophobic |
| N7 | O | ILE- 112 | 2.78 | 136.17 | H-Bond (Ligand Donor) |
| C11 | CD1 | ILE- 112 | 4.19 | 0 | Hydrophobic |
| C11 | C5N | NDP- 193 | 4.07 | 0 | Hydrophobic |
| C9 | C4N | NDP- 193 | 3.85 | 0 | Hydrophobic |
