sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2012-05-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.350 | 6.350 | 6.350 | 0.000 | 6.350 | 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: | 28.033 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.074 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 70.27 | 29.73 |
| According to VolSite | |
| HET Code: | ZYL |
|---|---|
| Formula: | C19H21NO5 |
| Molecular weight: | 343.374 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.48 % |
| Polar Surface area: | 92.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -23.7693 | 12.6208 | 6.90364 |
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 |
| OAB | NE2 | HIS- 18 | 2.93 | 151.59 | H-Bond (Protein Donor) |
| CAQ | CE2 | PHE- 22 | 4.16 | 0 | Hydrophobic |
| CAF | CB | ALA- 134 | 3.52 | 0 | Hydrophobic |
| CAF | CG2 | VAL- 137 | 3.74 | 0 | Hydrophobic |
| CAH | CB | VAL- 137 | 3.4 | 0 | Hydrophobic |
| CAP | CG1 | VAL- 137 | 4.45 | 0 | Hydrophobic |
| CAU | CG1 | VAL- 137 | 4.4 | 0 | Hydrophobic |
| CAL | CB | LEU- 141 | 3.99 | 0 | Hydrophobic |
| CAO | CD1 | LEU- 141 | 4.13 | 0 | Hydrophobic |
| CAA | CD1 | LEU- 145 | 4.02 | 0 | Hydrophobic |
| CAA | CB | ALA- 157 | 3.66 | 0 | Hydrophobic |
| CAM | CD2 | LEU- 160 | 3.4 | 0 | Hydrophobic |
| CAO | CD1 | LEU- 164 | 3.93 | 0 | Hydrophobic |
| CAQ | CB | LEU- 164 | 3.87 | 0 | Hydrophobic |
| CAA | CE1 | PHE- 233 | 3.53 | 0 | Hydrophobic |
| OAE | MG | MG- 304 | 2.66 | 0 | Metal Acceptor |
