sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.620 Å
X-ray
2014-06-03
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_HUMAN |
| AC: | P00374 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.036 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.750 | 384.750 |
| % Hydrophobic | % Polar |
|---|---|
| 60.53 | 39.47 |
| According to VolSite | |
| HET Code: | IXE |
|---|---|
| Formula: | C14H11F3N6 |
| Molecular weight: | 320.273 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.05 % |
| Polar Surface area: | 93.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -3.8513 | -15.8959 | -26.2804 |
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 |
| N6 | O | ILE- 7 | 2.94 | 159.84 | H-Bond (Ligand Donor) |
| N4 | O | VAL- 8 | 3.45 | 122.13 | H-Bond (Ligand Donor) |
| F1 | CB | ASP- 21 | 4.48 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 22 | 4.39 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 22 | 3.67 | 0 | Hydrophobic |
| C11 | CG | LEU- 22 | 3.99 | 0 | Hydrophobic |
| N4 | OE1 | GLU- 30 | 2.63 | 168.83 | H-Bond (Ligand Donor) |
| N4 | OE2 | GLU- 30 | 3.46 | 130.54 | H-Bond (Ligand Donor) |
| N3 | OE2 | GLU- 30 | 2.75 | 170.34 | H-Bond (Ligand Donor) |
| F3 | CE1 | PHE- 31 | 4.46 | 0 | Hydrophobic |
| C1 | CG2 | THR- 56 | 3.89 | 0 | Hydrophobic |
| F1 | CB | SER- 59 | 3.95 | 0 | Hydrophobic |
| F2 | CG | PRO- 61 | 4.28 | 0 | Hydrophobic |
| F3 | CG | PRO- 61 | 3.91 | 0 | Hydrophobic |
| C1 | C5N | NDP- 201 | 3.3 | 0 | Hydrophobic |
| N4 | O | HOH- 301 | 3.42 | 144.02 | H-Bond (Ligand Donor) |
