sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2009-01-08
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_STAAU |
| AC: | P0A017 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 1280 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| X | 100 % |
| B-Factor: | 37.297 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.374 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 63.58 | 36.42 |
| According to VolSite | |
| HET Code: | DHF |
|---|---|
| Formula: | C19H19N7O6 |
| Molecular weight: | 441.397 g/mol |
| DrugBank ID: | DB02015 |
| Buried Surface Area: | 58.73 % |
| Polar Surface area: | 213.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 32.298 | 9.77784 | 40.791 |
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 |
| NA2 | OD2 | ASP- 27 | 3.27 | 148.22 | H-Bond (Ligand Donor) |
| CG | CB | LEU- 28 | 4.03 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 28 | 3.55 | 0 | Hydrophobic |
| CB | CB | LYS- 32 | 4.2 | 0 | Hydrophobic |
| C9 | CG2 | THR- 46 | 4.33 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 50 | 4.11 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 50 | 4.19 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 50 | 4.13 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 54 | 4.2 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 54 | 3.53 | 0 | Hydrophobic |
| O1 | CZ | ARG- 57 | 3.8 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 57 | 3.31 | 0 | Ionic (Protein Cationic) |
| O1 | NH2 | ARG- 57 | 2.81 | 142.96 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 57 | 3.1 | 128.35 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 57 | 2.72 | 141.87 | H-Bond (Protein Donor) |
| C9 | CE1 | PHE- 92 | 3.56 | 0 | Hydrophobic |
| C15 | CZ | PHE- 92 | 3.35 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 92 | 3.87 | 0 | Aromatic Face/Face |
| NA2 | OG1 | THR- 111 | 3.45 | 144.76 | H-Bond (Ligand Donor) |
| C9 | C4N | NDP- 301 | 4.02 | 0 | Hydrophobic |
