sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
1995-08-01
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_LACCA |
| AC: | P00381 |
| Organism: | Lactobacillus casei |
| Reign: | Bacteria |
| TaxID: | 1582 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.288 | 789.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.41 | 43.59 |
| According to VolSite | |
| HET Code: | BDM |
|---|---|
| Formula: | C20H23BrN4O6 |
| Molecular weight: | 495.324 g/mol |
| DrugBank ID: | DB02809 |
| Buried Surface Area: | 58.4 % |
| Polar Surface area: | 176.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -2.72806 | 35.5125 | 22.5072 |
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 |
| C7 | CD2 | LEU- 19 | 4.21 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 19 | 3.61 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 19 | 3.71 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 26 | 2.94 | 125.77 | H-Bond (Ligand Donor) |
| C9 | CG | LEU- 27 | 4.18 | 0 | Hydrophobic |
| BR11 | CD2 | LEU- 27 | 3.89 | 0 | Hydrophobic |
| C15 | CG | LEU- 27 | 4.18 | 0 | Hydrophobic |
| C20 | CB | LEU- 27 | 4.25 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 27 | 3.73 | 0 | Hydrophobic |
| C7 | CE1 | PHE- 30 | 4.02 | 0 | Hydrophobic |
| C15 | CE2 | PHE- 30 | 3.58 | 0 | Hydrophobic |
| C16 | CD2 | PHE- 30 | 4.25 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 30 | 3.23 | 0 | Hydrophobic |
| C17 | CB | ARG- 31 | 4.2 | 0 | Hydrophobic |
| C19 | CD | ARG- 31 | 4.12 | 0 | Hydrophobic |
| OXV | CZ | ARG- 31 | 3.69 | 0 | Ionic (Protein Cationic) |
| OXW | CZ | ARG- 31 | 3.83 | 0 | Ionic (Protein Cationic) |
| C14 | CB | SER- 48 | 3.93 | 0 | Hydrophobic |
| BR11 | CD1 | PHE- 49 | 4.28 | 0 | Hydrophobic |
| C14 | CD1 | PHE- 49 | 4.09 | 0 | Hydrophobic |
| BR11 | CG | PRO- 50 | 3.77 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 54 | 4 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 54 | 3.97 | 0 | Hydrophobic |
| OXW | CZ | ARG- 57 | 3.96 | 0 | Ionic (Protein Cationic) |
