sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.410 Å
X-ray
2009-07-09
| 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: | 12.178 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.445 | 408.375 |
| % Hydrophobic | % Polar |
|---|---|
| 68.60 | 31.40 |
| According to VolSite | |
| HET Code: | N22 |
|---|---|
| Formula: | C17H20N4O2 |
| Molecular weight: | 312.366 g/mol |
| DrugBank ID: | DB08234 |
| Buried Surface Area: | 72.93 % |
| Polar Surface area: | 96.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -29.8062 | -11.4877 | 42.5683 |
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 |
| N7 | O | LEU- 5 | 2.72 | 156.71 | H-Bond (Ligand Donor) |
| C15 | CG | LEU- 20 | 4.19 | 0 | Hydrophobic |
| C2 | CG | LEU- 20 | 4.34 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 20 | 3.77 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 20 | 4.16 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 20 | 4 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 20 | 4.07 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 27 | 3.42 | 132.88 | H-Bond (Ligand Donor) |
| N4 | OD1 | ASP- 27 | 2.66 | 169.2 | H-Bond (Ligand Donor) |
| N8 | OD2 | ASP- 27 | 2.87 | 161.29 | H-Bond (Ligand Donor) |
| C8 | CG | LEU- 28 | 4.15 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 28 | 3.85 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 31 | 4.02 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 31 | 4.44 | 0 | Hydrophobic |
| C11 | CG2 | THR- 46 | 3.74 | 0 | Hydrophobic |
| C2 | CB | SER- 49 | 3.86 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 50 | 4.15 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 50 | 4.49 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 50 | 3.66 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 54 | 4.01 | 0 | Hydrophobic |
| N7 | O | PHE- 92 | 3.05 | 131.73 | H-Bond (Ligand Donor) |
| C9 | CZ | PHE- 92 | 3.67 | 0 | Hydrophobic |
| C10 | CE1 | PHE- 92 | 3.71 | 0 | Hydrophobic |
| C11 | C5N | NDP- 207 | 3.67 | 0 | Hydrophobic |
| C2 | C2D | NDP- 207 | 3.83 | 0 | Hydrophobic |
| C10 | C4N | NDP- 207 | 3.28 | 0 | Hydrophobic |
