sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2009-01-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 10.090 | 10.100 | 10.100 | 0.000 | 10.100 | 2 |
| 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: | 45.854 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.029 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 63.78 | 36.22 |
| According to VolSite | |
| HET Code: | XCF |
|---|---|
| Formula: | C19H22N4O3 |
| Molecular weight: | 354.403 g/mol |
| DrugBank ID: | DB08741 |
| Buried Surface Area: | 60.25 % |
| Polar Surface area: | 105.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 30.8045 | 11.615 | 42.2295 |
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 | 2.68 | 157.85 | H-Bond (Ligand Donor) |
| C21 | CG | LEU- 20 | 4.14 | 0 | Hydrophobic |
| C20 | CG | LEU- 20 | 4.02 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 20 | 3.73 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 27 | 2.93 | 149.51 | H-Bond (Ligand Donor) |
| N4 | OD1 | ASP- 27 | 3.08 | 139.13 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 27 | 2.88 | 148.48 | H-Bond (Ligand Donor) |
| C14 | CD2 | LEU- 28 | 3.44 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 28 | 4.3 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 31 | 4.3 | 0 | Hydrophobic |
| C20 | CB | SER- 49 | 4.31 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 50 | 4.37 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 50 | 4.27 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 54 | 4.5 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 54 | 3.63 | 0 | Hydrophobic |
| N7 | O | PHE- 92 | 2.74 | 136.59 | H-Bond (Ligand Donor) |
| C9 | CZ | PHE- 92 | 3.32 | 0 | Hydrophobic |
| C9 | C4N | NDP- 301 | 3.52 | 0 | Hydrophobic |
| C20 | C2D | NDP- 301 | 3.44 | 0 | Hydrophobic |
