sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
1996-11-26
| 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 | 94 % |
| B | 6 % |
| B-Factor: | 17.409 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.105 | 1032.750 |
| % Hydrophobic | % Polar |
|---|---|
| 37.58 | 62.42 |
| According to VolSite | |
| HET Code: | MTX |
|---|---|
| Formula: | C20H20N8O5 |
| Molecular weight: | 452.423 g/mol |
| DrugBank ID: | DB00563 |
| Buried Surface Area: | 48.45 % |
| Polar Surface area: | 216.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 7.79842 | 51.7285 | 18.7198 |
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 |
| NA4 | O | ILE- 5 | 2.87 | 154.07 | H-Bond (Ligand Donor) |
| NA2 | OD1 | ASP- 27 | 2.95 | 170.93 | H-Bond (Ligand Donor) |
| NA2 | OD2 | ASP- 27 | 3.28 | 121.85 | H-Bond (Ligand Donor) |
| C16 | CD2 | LEU- 28 | 3.93 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 31 | 3.45 | 0 | Hydrophobic |
| CB | CD | LYS- 32 | 4.33 | 0 | Hydrophobic |
| C9 | CG2 | THR- 46 | 4.27 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 50 | 3.95 | 0 | Hydrophobic |
| CM | CG1 | ILE- 50 | 4.35 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 50 | 3.65 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 54 | 4.12 | 0 | Hydrophobic |
| O1 | CZ | ARG- 57 | 3.86 | 0 | Ionic (Protein Cationic) |
| O1 | NH1 | ARG- 57 | 3.22 | 162.3 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 57 | 3.09 | 163.27 | H-Bond (Protein Donor) |
| NA4 | O | ILE- 94 | 2.97 | 138.69 | H-Bond (Ligand Donor) |
| NA2 | O | HOH- 409 | 2.89 | 134.62 | H-Bond (Ligand Donor) |
