sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.480 Å
X-ray
2009-01-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.290 | 8.590 | 8.470 | 0.270 | 8.920 | 5 |
| 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: | 10.710 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.226 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 53.01 | 46.99 |
| According to VolSite | |
| HET Code: | TOP |
|---|---|
| Formula: | C14H18N4O3 |
| Molecular weight: | 290.318 g/mol |
| DrugBank ID: | DB00440 |
| Buried Surface Area: | 53.1 % |
| Polar Surface area: | 105.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 8.60086 | -5.427 | 15.9327 |
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 | 2.84 | 168.86 | H-Bond (Ligand Donor) |
| C14 | CG | LEU- 20 | 3.9 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 20 | 3.9 | 0 | Hydrophobic |
| C12 | CG | LEU- 20 | 3.64 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 20 | 4.14 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 20 | 4.32 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 20 | 3.83 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 27 | 2.71 | 174.81 | H-Bond (Ligand Donor) |
| N4 | OD1 | ASP- 27 | 2.85 | 174.84 | H-Bond (Ligand Donor) |
| N4 | OD2 | ASP- 27 | 3.4 | 130.17 | H-Bond (Ligand Donor) |
| C20 | CD2 | LEU- 28 | 3.94 | 0 | Hydrophobic |
| C14 | CB | SER- 49 | 4.14 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 50 | 4 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 50 | 3.7 | 0 | Hydrophobic |
| N7 | O | PHE- 92 | 2.88 | 131.97 | H-Bond (Ligand Donor) |
| C9 | CZ | PHE- 92 | 3.63 | 0 | Hydrophobic |
| N4 | O | HOH- 2062 | 3.24 | 139.25 | H-Bond (Ligand Donor) |
