sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.010 Å
X-ray
2010-03-02
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 16.859 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.447 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 69.53 | 30.47 |
| According to VolSite | |
| HET Code: | RAR |
|---|---|
| Formula: | C27H30N6O3 |
| Molecular weight: | 486.565 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.68 % |
| Polar Surface area: | 128.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -7.34925 | 33.6873 | -4.70564 |
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 |
| N01 | O | LEU- 5 | 2.82 | 157.2 | H-Bond (Ligand Donor) |
| C07 | CG | LEU- 20 | 3.82 | 0 | Hydrophobic |
| C09 | CG | LEU- 20 | 3.98 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 20 | 3.67 | 0 | Hydrophobic |
| C06 | CD2 | LEU- 20 | 3.86 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 20 | 3.87 | 0 | Hydrophobic |
| N35 | OD1 | ASP- 27 | 3.17 | 151.89 | H-Bond (Ligand Donor) |
| N35 | OD2 | ASP- 27 | 2.79 | 144.15 | H-Bond (Ligand Donor) |
| C12 | CD1 | LEU- 28 | 4.42 | 0 | Hydrophobic |
| C21 | CB | LEU- 28 | 3.89 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 28 | 3.91 | 0 | Hydrophobic |
| C23 | CG | LYS- 29 | 3.61 | 0 | Hydrophobic |
| C03 | CG2 | VAL- 31 | 4.28 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 31 | 3.97 | 0 | Hydrophobic |
| C23 | CD | LYS- 32 | 3.94 | 0 | Hydrophobic |
| C19 | CB | LYS- 32 | 3.53 | 0 | Hydrophobic |
| C26 | CG | LYS- 32 | 3.53 | 0 | Hydrophobic |
| C28 | CD | LYS- 32 | 4.34 | 0 | Hydrophobic |
| C09 | CB | SER- 49 | 4.11 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 50 | 3.66 | 0 | Hydrophobic |
| C06 | CD1 | ILE- 50 | 4.33 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 54 | 4 | 0 | Hydrophobic |
| C26 | CB | LEU- 54 | 4.31 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 54 | 4.27 | 0 | Hydrophobic |
| C28 | CG | PRO- 55 | 3.68 | 0 | Hydrophobic |
| N01 | O | PHE- 92 | 2.81 | 135.15 | H-Bond (Ligand Donor) |
| C04 | CZ | PHE- 92 | 3.49 | 0 | Hydrophobic |
| N35 | O | HOH- 173 | 3.2 | 145.72 | H-Bond (Ligand Donor) |
| C09 | C2D | NAP- 201 | 3.65 | 0 | Hydrophobic |
| C04 | C4N | NAP- 201 | 3.59 | 0 | Hydrophobic |
| C06 | C5N | NAP- 201 | 4.03 | 0 | Hydrophobic |
