sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.200 Å
X-ray
2015-07-01
| 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: | 17.813 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.217 | 597.375 |
| % Hydrophobic | % Polar |
|---|---|
| 61.58 | 38.42 |
| According to VolSite | |
| HET Code: | DDF |
|---|---|
| Formula: | C21H23N5O6 |
| Molecular weight: | 441.437 g/mol |
| DrugBank ID: | DB12769 |
| Buried Surface Area: | 51.84 % |
| Polar Surface area: | 188.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -21.728 | 0.284594 | 6.01816 |
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 |
| N8 | O | ILE- 5 | 3.21 | 151.19 | H-Bond (Ligand Donor) |
| NA2 | OD2 | ASP- 27 | 3.48 | 126.34 | H-Bond (Ligand Donor) |
| NA2 | OD1 | ASP- 27 | 3.02 | 167.05 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 27 | 2.75 | 155.12 | H-Bond (Ligand Donor) |
| CG | CD2 | PHE- 28 | 3.56 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 31 | 3.92 | 0 | Hydrophobic |
| CB | CD | LYS- 32 | 4.21 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 50 | 4.31 | 0 | Hydrophobic |
| C13 | CG1 | ILE- 50 | 3.82 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 54 | 3.84 | 0 | Hydrophobic |
| O1 | NH1 | ARG- 57 | 2.6 | 168.41 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 57 | 3.25 | 128.51 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 57 | 2.52 | 166.01 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 57 | 3.34 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 57 | 3.45 | 0 | Ionic (Protein Cationic) |
| C7 | CB | ILE- 94 | 4.46 | 0 | Hydrophobic |
| O4 | O | HOH- 350 | 2.82 | 145.66 | H-Bond (Protein Donor) |
