sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.090 Å
X-ray
2011-03-03
| 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: | 7.183 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.956 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 64.76 | 35.24 |
| According to VolSite | |
| HET Code: | Q24 |
|---|---|
| Formula: | C8H8N4 |
| Molecular weight: | 160.176 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 74.49 % |
| Polar Surface area: | 77.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 2.46433 | -3.55392 | -10.6525 |
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 | 2.9 | 171.09 | H-Bond (Ligand Donor) |
| C4A | CE | MET- 20 | 4.19 | 0 | Hydrophobic |
| C6 | SD | MET- 20 | 4.4 | 0 | Hydrophobic |
| C8 | CE | MET- 20 | 3.48 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 27 | 2.68 | 154.42 | H-Bond (Ligand Donor) |
| NA2 | OD1 | ASP- 27 | 2.81 | 165.49 | H-Bond (Ligand Donor) |
| NA2 | OD2 | ASP- 27 | 3.48 | 126.26 | H-Bond (Ligand Donor) |
| C8 | CD2 | LEU- 28 | 3.53 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 31 | 3.76 | 0 | Hydrophobic |
| C6 | CE2 | PHE- 31 | 4.03 | 0 | Hydrophobic |
| C7 | CD2 | PHE- 31 | 4.16 | 0 | Hydrophobic |
| C8 | CG | PHE- 31 | 4.17 | 0 | Hydrophobic |
| C4A | CD1 | PHE- 31 | 3.45 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 50 | 4.43 | 0 | Hydrophobic |
| NA4 | O | ILE- 94 | 3.01 | 137.71 | H-Bond (Ligand Donor) |
| C5 | C4N | NDP- 1160 | 3.81 | 0 | Hydrophobic |
