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: | 10.590 | 10.590 | 10.590 | 0.000 | 10.590 | 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: | 16.798 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.376 | 415.125 |
| % Hydrophobic | % Polar |
|---|---|
| 69.11 | 30.89 |
| According to VolSite | |
| HET Code: | Q27 |
|---|---|
| Formula: | C21H20N4O |
| Molecular weight: | 344.410 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.2 % |
| Polar Surface area: | 87.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -5.14662 | -32.1213 | 6.06596 |
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 | 2.73 | 169.49 | H-Bond (Ligand Donor) |
| C25 | CG | LEU- 21 | 3.73 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 21 | 4 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 21 | 3.81 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 28 | 2.77 | 162.81 | H-Bond (Ligand Donor) |
| N12 | OD2 | ASP- 28 | 3.2 | 135.87 | H-Bond (Ligand Donor) |
| N12 | OD1 | ASP- 28 | 2.73 | 163.21 | H-Bond (Ligand Donor) |
| C7 | CD2 | LEU- 29 | 4.03 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 29 | 3.85 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 29 | 3.68 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 29 | 4.21 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 32 | 4.35 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 4.35 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 32 | 4.42 | 0 | Hydrophobic |
| C13 | CG2 | THR- 47 | 3.61 | 0 | Hydrophobic |
| C26 | CG2 | THR- 47 | 4.35 | 0 | Hydrophobic |
| C26 | CB | SER- 50 | 3.75 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 51 | 3.67 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 51 | 3.99 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 55 | 4.15 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 55 | 4.01 | 0 | Hydrophobic |
| N11 | O | PHE- 93 | 2.82 | 151.93 | H-Bond (Ligand Donor) |
| C13 | CE2 | PHE- 93 | 3.36 | 0 | Hydrophobic |
| C10 | CZ | PHE- 93 | 3.34 | 0 | Hydrophobic |
| C13 | C5N | NAP- 169 | 4.07 | 0 | Hydrophobic |
| C26 | C2D | NAP- 169 | 3.33 | 0 | Hydrophobic |
| N12 | O | HOH- 187 | 3.17 | 141.39 | H-Bond (Ligand Donor) |
