sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.680 Å
X-ray
2011-07-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.460 | 9.460 | 9.460 | 0.000 | 9.460 | 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: | 17.629 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.840 | 297.000 |
| % Hydrophobic | % Polar |
|---|---|
| 65.91 | 34.09 |
| According to VolSite | |
| HET Code: | Q12 |
|---|---|
| Formula: | C17H18N4O2 |
| Molecular weight: | 310.350 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.1 % |
| Polar Surface area: | 96.28 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: | 3 |
| X | Y | Z |
|---|---|---|
| 6.0283 | -32.0453 | -6.24104 |
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 | 2.75 | 171.63 | H-Bond (Ligand Donor) |
| C14 | CD1 | LEU- 21 | 4.26 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 21 | 3.83 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 21 | 4.22 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 21 | 3.73 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 28 | 2.66 | 169.55 | H-Bond (Ligand Donor) |
| N12 | OD2 | ASP- 28 | 3.4 | 128.88 | H-Bond (Ligand Donor) |
| N12 | OD1 | ASP- 28 | 2.81 | 176.72 | H-Bond (Ligand Donor) |
| C10 | CD1 | LEU- 29 | 3.78 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 29 | 3.45 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 32 | 4.31 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 32 | 4.26 | 0 | Hydrophobic |
| C13 | CG2 | THR- 47 | 4.26 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 51 | 3.77 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 51 | 4.44 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 51 | 3.91 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 55 | 3.35 | 0 | Hydrophobic |
| N11 | O | PHE- 93 | 2.82 | 142.2 | H-Bond (Ligand Donor) |
| C13 | CE2 | PHE- 93 | 3.58 | 0 | Hydrophobic |
| C7 | CZ | PHE- 93 | 3.3 | 0 | Hydrophobic |
| C13 | C5N | NAP- 168 | 4.37 | 0 | Hydrophobic |
| N12 | O | HOH- 177 | 3.1 | 138.82 | H-Bond (Ligand Donor) |
