sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.150 Å
X-ray
2013-05-03
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_ECOLI |
| AC: | P0ABQ4 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 5.811 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.272 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 66.98 | 33.02 |
| According to VolSite | |
| HET Code: | FOL |
|---|---|
| Formula: | C19H17N7O6 |
| Molecular weight: | 439.382 g/mol |
| DrugBank ID: | DB00158 |
| Buried Surface Area: | 60.17 % |
| Polar Surface area: | 214.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| 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 |
|---|---|---|
| 1.06456 | -3.52013 | -7.71844 |
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 |
| C9 | CE | MET- 20 | 4.41 | 0 | Hydrophobic |
| C13 | CE | MET- 20 | 3.61 | 0 | Hydrophobic |
| NA2 | OD1 | ASP- 27 | 3 | 168.2 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 27 | 2.66 | 156.59 | H-Bond (Ligand Donor) |
| CG | CB | LEU- 28 | 3.84 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 28 | 4.02 | 0 | Hydrophobic |
| CG | CB | LYS- 32 | 4.07 | 0 | Hydrophobic |
| C9 | CG2 | THR- 46 | 4.17 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 50 | 4.4 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 50 | 4.13 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 50 | 3.78 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 54 | 3.81 | 0 | Hydrophobic |
| O1 | NH1 | ARG- 57 | 2.83 | 162.76 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 57 | 3.43 | 131.05 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 57 | 2.9 | 173.21 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 57 | 3.56 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 57 | 3.8 | 0 | Ionic (Protein Cationic) |
| C9 | C4N | NAP- 202 | 3.57 | 0 | Hydrophobic |
| O4 | O | HOH- 306 | 2.79 | 147.34 | H-Bond (Protein Donor) |
| NA2 | O | HOH- 606 | 2.95 | 145.2 | H-Bond (Ligand Donor) |
