sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2012-05-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.600 | 6.600 | 6.600 | 0.000 | 6.600 | 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: | 27.135 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.715 | 1110.375 |
| % Hydrophobic | % Polar |
|---|---|
| 37.69 | 62.31 |
| According to VolSite | |
| HET Code: | ZYM |
|---|---|
| Formula: | C19H18NO5 |
| Molecular weight: | 340.350 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.42 % |
| Polar Surface area: | 95.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 26.3516 | -10.3091 | 8.21448 |
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 |
| CAF | CE | MET- 15 | 3.78 | 0 | Hydrophobic |
| CAH | CB | PHE- 22 | 3.93 | 0 | Hydrophobic |
| CAF | CG1 | VAL- 37 | 4.19 | 0 | Hydrophobic |
| CAM | CE2 | TYR- 41 | 3.34 | 0 | Hydrophobic |
| CAG | CB | TYR- 41 | 3.68 | 0 | Hydrophobic |
| CAI | CB | CYS- 44 | 3.68 | 0 | Hydrophobic |
| CAW | CB | CYS- 44 | 3.85 | 0 | Hydrophobic |
| CAI | CB | ARG- 45 | 4.27 | 0 | Hydrophobic |
| CAJ | CB | ASP- 48 | 4.24 | 0 | Hydrophobic |
| CAO | CB | ASP- 48 | 4.04 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 107 | 4.16 | 0 | Hydrophobic |
| CAN | CG2 | VAL- 137 | 3.84 | 0 | Hydrophobic |
| CAY | CG1 | VAL- 137 | 4.2 | 0 | Hydrophobic |
| CAK | CG1 | VAL- 137 | 3.5 | 0 | Hydrophobic |
| CAG | CD1 | LEU- 141 | 3.83 | 0 | Hydrophobic |
| OAA | NH2 | ARG- 171 | 3.48 | 137.01 | H-Bond (Protein Donor) |
| OAC | MG | MG- 305 | 2.44 | 0 | Metal Acceptor |
| OAD | MG | MG- 305 | 2.54 | 0 | Metal Acceptor |
