sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2011-06-15
| 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: | 56.523 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.946 | 452.250 |
| % Hydrophobic | % Polar |
|---|---|
| 66.42 | 33.58 |
| According to VolSite | |
| HET Code: | 5DR |
|---|---|
| Formula: | C22H22N4O |
| Molecular weight: | 358.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.6 % |
| Polar Surface area: | 87.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -10.7395 | -31.5836 | 6.56093 |
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 |
| NAD | O | LEU- 5 | 2.77 | 157.97 | H-Bond (Ligand Donor) |
| CAB | CG | LEU- 20 | 3.67 | 0 | Hydrophobic |
| CAO | CD1 | LEU- 20 | 3.78 | 0 | Hydrophobic |
| CAE | CD2 | LEU- 20 | 4.32 | 0 | Hydrophobic |
| CAX | CD1 | LEU- 20 | 4.33 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 27 | 2.77 | 161.28 | H-Bond (Ligand Donor) |
| NAC | OD2 | ASP- 27 | 3.11 | 164.89 | H-Bond (Ligand Donor) |
| CAA | CD2 | LEU- 28 | 3.47 | 0 | Hydrophobic |
| CAI | CD2 | LEU- 28 | 3.7 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 31 | 4.5 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 31 | 4.2 | 0 | Hydrophobic |
| CAP | CG2 | THR- 46 | 3.87 | 0 | Hydrophobic |
| CAB | CB | SER- 49 | 4.25 | 0 | Hydrophobic |
| CAP | CD1 | ILE- 50 | 4.21 | 0 | Hydrophobic |
| CAZ | CG1 | ILE- 50 | 3.62 | 0 | Hydrophobic |
| CAH | CD2 | LEU- 54 | 3.7 | 0 | Hydrophobic |
| CAF | CZ | PHE- 92 | 3.57 | 0 | Hydrophobic |
| CAE | CE1 | PHE- 92 | 3.51 | 0 | Hydrophobic |
| CAB | C2D | NDP- 207 | 3.78 | 0 | Hydrophobic |
| CAP | C5N | NDP- 207 | 3.75 | 0 | Hydrophobic |
| CAE | C4N | NDP- 207 | 3.36 | 0 | Hydrophobic |
