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: | 10.700 | 10.700 | 10.700 | 0.000 | 10.700 | 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: | 14.797 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.058 | 421.875 |
| % Hydrophobic | % Polar |
|---|---|
| 66.40 | 33.60 |
| According to VolSite | |
| HET Code: | Q26 |
|---|---|
| Formula: | C23H23N5O3S |
| Molecular weight: | 449.525 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.73 % |
| Polar Surface area: | 141.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -6.39959 | 33.1605 | -5.39578 |
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 | 2.72 | 176.85 | H-Bond (Ligand Donor) |
| C20 | CG | LEU- 21 | 3.94 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 21 | 4.28 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 21 | 3.89 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 28 | 2.72 | 164.59 | H-Bond (Ligand Donor) |
| N12 | OD1 | ASP- 28 | 2.72 | 164.73 | H-Bond (Ligand Donor) |
| N12 | OD2 | ASP- 28 | 3.24 | 134.13 | H-Bond (Ligand Donor) |
| C7 | CD2 | LEU- 29 | 4.05 | 0 | Hydrophobic |
| C32 | CB | LEU- 29 | 3.79 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 29 | 3.61 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 29 | 3.76 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 29 | 3.98 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 4.42 | 0 | Hydrophobic |
| C32 | CB | LYS- 33 | 3.92 | 0 | Hydrophobic |
| C21 | CG2 | THR- 47 | 4.48 | 0 | Hydrophobic |
| C21 | CB | SER- 50 | 3.77 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 51 | 4.47 | 0 | Hydrophobic |
| C20 | CG1 | ILE- 51 | 4.37 | 0 | Hydrophobic |
| C17 | CG1 | ILE- 51 | 3.89 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 55 | 3.76 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 55 | 3.76 | 0 | Hydrophobic |
| O30 | NH2 | ARG- 58 | 3.17 | 133.76 | H-Bond (Protein Donor) |
| O30 | NH1 | ARG- 58 | 2.79 | 152.39 | H-Bond (Protein Donor) |
| N11 | O | PHE- 93 | 2.81 | 154.99 | H-Bond (Ligand Donor) |
| C10 | CZ | PHE- 93 | 3.27 | 0 | Hydrophobic |
| C21 | C2D | NAP- 168 | 3.48 | 0 | Hydrophobic |
| N12 | O | HOH- 173 | 3.24 | 142.93 | H-Bond (Ligand Donor) |
