sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.070 Å
X-ray
2011-08-16
| 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: | 27.049 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.782 | 1123.875 |
| % Hydrophobic | % Polar |
|---|---|
| 37.24 | 62.76 |
| According to VolSite | |
| HET Code: | 2CJ |
|---|---|
| Formula: | C26H32N2O3 |
| Molecular weight: | 420.544 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.66 % |
| Polar Surface area: | 64.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 1.11858 | 26.3314 | 6.36206 |
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 |
| CAE | CE | MET- 15 | 3.79 | 0 | Hydrophobic |
| CAU | CB | SER- 19 | 3.29 | 0 | Hydrophobic |
| CAH | CB | PHE- 22 | 4.2 | 0 | Hydrophobic |
| CAT | CE2 | PHE- 22 | 3.9 | 0 | Hydrophobic |
| CAW | CE2 | PHE- 22 | 3.65 | 0 | Hydrophobic |
| CAH | CE2 | PHE- 26 | 3.4 | 0 | Hydrophobic |
| CAE | CG1 | VAL- 37 | 3.73 | 0 | Hydrophobic |
| CAI | CB | TYR- 41 | 3.75 | 0 | Hydrophobic |
| CAJ | CG1 | VAL- 137 | 4 | 0 | Hydrophobic |
| CAM | CG1 | VAL- 137 | 3.24 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 141 | 4.22 | 0 | Hydrophobic |
| CAI | CD1 | LEU- 141 | 3.72 | 0 | Hydrophobic |
| CAD | CD2 | LEU- 160 | 3.86 | 0 | Hydrophobic |
| CAK | CD1 | LEU- 164 | 3.52 | 0 | Hydrophobic |
| OAB | ND2 | ASN- 168 | 2.7 | 153.48 | H-Bond (Protein Donor) |
| OAA | NH2 | ARG- 171 | 3.19 | 132.89 | H-Bond (Protein Donor) |
| OAC | NH2 | ARG- 171 | 3.34 | 124.11 | H-Bond (Protein Donor) |
| OAA | CZ | ARG- 171 | 3.97 | 0 | Ionic (Protein Cationic) |
| CAT | CZ | TYR- 248 | 3.65 | 0 | Hydrophobic |
