sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2012-03-21
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.440 | 6.440 | 6.440 | 0.000 | 6.440 | 1 |
| Name: | Dehydrosqualene synthase |
|---|---|
| ID: | CRTM_STAAU |
| AC: | A9JQL9 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 1280 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 42.077 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.885 | 641.250 |
| % Hydrophobic | % Polar |
|---|---|
| 54.21 | 45.79 |
| According to VolSite | |
| HET Code: | RWZ |
|---|---|
| Formula: | C22H39N2 |
| Molecular weight: | 331.558 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.8 % |
| Polar Surface area: | 28.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -23.5225 | -16.0459 | -7.75733 |
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 |
| CAB | CE1 | PHE- 22 | 4.23 | 0 | Hydrophobic |
| CAJ | CZ | PHE- 22 | 4.29 | 0 | Hydrophobic |
| CAB | CE2 | PHE- 26 | 4.11 | 0 | Hydrophobic |
| CAN | CZ | TYR- 41 | 4.06 | 0 | Hydrophobic |
| CAU | CB | CYS- 44 | 3.21 | 0 | Hydrophobic |
| CAK | CB | ARG- 45 | 4.33 | 0 | Hydrophobic |
| CAT | CD | ARG- 45 | 4.49 | 0 | Hydrophobic |
| CAL | CB | ASP- 48 | 3.83 | 0 | Hydrophobic |
| CAM | CD1 | LEU- 107 | 4.1 | 0 | Hydrophobic |
| CAV | CG1 | VAL- 133 | 4.36 | 0 | Hydrophobic |
| CAC | CB | ALA- 134 | 3.49 | 0 | Hydrophobic |
| CAC | CB | VAL- 137 | 3.78 | 0 | Hydrophobic |
| CAF | CG1 | VAL- 137 | 3.51 | 0 | Hydrophobic |
| CAO | CG2 | VAL- 137 | 3.89 | 0 | Hydrophobic |
| CAA | CD1 | LEU- 141 | 4.37 | 0 | Hydrophobic |
| CAB | CD1 | LEU- 141 | 4.49 | 0 | Hydrophobic |
| CAA | CD2 | LEU- 160 | 3.56 | 0 | Hydrophobic |
| CAA | CD1 | LEU- 164 | 4.31 | 0 | Hydrophobic |
| CAB | CD1 | LEU- 164 | 3.5 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 164 | 3.8 | 0 | Hydrophobic |
| NAQ | OE1 | GLN- 165 | 3.34 | 143.81 | H-Bond (Ligand Donor) |
| NAP | OH | TYR- 248 | 3.33 | 136.31 | H-Bond (Ligand Donor) |
