sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.690 Å
X-ray
2011-07-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.320 | 9.320 | 9.320 | 0.000 | 9.320 | 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: | 18.445 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.431 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 68.06 | 31.94 |
| According to VolSite | |
| HET Code: | Q19 |
|---|---|
| Formula: | C17H16N4O |
| Molecular weight: | 292.335 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.54 % |
| Polar Surface area: | 94.88 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: | 2 |
| X | Y | Z |
|---|---|---|
| -5.85214 | -31.9456 | 5.79559 |
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 | 2.74 | 174.6 | H-Bond (Ligand Donor) |
| C9 | CD1 | LEU- 21 | 4.38 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 21 | 3.76 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 21 | 3.67 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 28 | 2.64 | 167.96 | H-Bond (Ligand Donor) |
| N12 | OD2 | ASP- 28 | 3.34 | 128.69 | H-Bond (Ligand Donor) |
| N12 | OD1 | ASP- 28 | 2.8 | 174.96 | H-Bond (Ligand Donor) |
| C7 | CD1 | LEU- 29 | 4.03 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 29 | 4 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 29 | 4.09 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 32 | 4.37 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 4.33 | 0 | Hydrophobic |
| C13 | CG2 | THR- 47 | 4.14 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 51 | 3.82 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 51 | 4.41 | 0 | Hydrophobic |
| N11 | O | PHE- 93 | 2.81 | 145.59 | H-Bond (Ligand Donor) |
| C13 | CE2 | PHE- 93 | 3.44 | 0 | Hydrophobic |
| C10 | CZ | PHE- 93 | 3.18 | 0 | Hydrophobic |
| C13 | C5N | NAP- 168 | 4.36 | 0 | Hydrophobic |
| N12 | O | HOH- 185 | 3.16 | 137.52 | H-Bond (Ligand Donor) |
