sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2011-07-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.620 | 9.620 | 9.620 | 0.000 | 9.620 | 1 |
| 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: | 15.407 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.310 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 75.22 | 24.78 |
| According to VolSite | |
| HET Code: | Q20 |
|---|---|
| Formula: | C18H18N4O2 |
| Molecular weight: | 322.361 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.62 % |
| Polar Surface area: | 104.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 5.06733 | -31.9487 | -6.24012 |
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 |
| N11 | O | LEU- 6 | 2.76 | 170.33 | H-Bond (Ligand Donor) |
| C21 | CG | LEU- 21 | 3.84 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 21 | 3.88 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 21 | 3.71 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 28 | 2.74 | 162.74 | H-Bond (Ligand Donor) |
| N12 | OD2 | ASP- 28 | 3.18 | 135.51 | H-Bond (Ligand Donor) |
| N12 | OD1 | ASP- 28 | 2.7 | 163.06 | H-Bond (Ligand Donor) |
| C10 | CD2 | LEU- 29 | 3.89 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 29 | 3.51 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 32 | 4.41 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 32 | 4.41 | 0 | Hydrophobic |
| C13 | CG2 | THR- 47 | 3.75 | 0 | Hydrophobic |
| C22 | CG2 | THR- 47 | 4.39 | 0 | Hydrophobic |
| C22 | CB | SER- 50 | 3.77 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 51 | 3.71 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 51 | 3.86 | 0 | Hydrophobic |
| N11 | O | PHE- 93 | 2.8 | 149.33 | H-Bond (Ligand Donor) |
| C13 | CE2 | PHE- 93 | 3.39 | 0 | Hydrophobic |
| C7 | CZ | PHE- 93 | 3.32 | 0 | Hydrophobic |
| C13 | C5N | NAP- 169 | 4.08 | 0 | Hydrophobic |
| C22 | C2D | NAP- 169 | 3.32 | 0 | Hydrophobic |
| N12 | O | HOH- 183 | 3.16 | 142.39 | H-Bond (Ligand Donor) |
