sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2000-05-10
| Name: | Squalene synthase |
|---|---|
| ID: | FDFT_HUMAN |
| AC: | P37268 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.5.1.21 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.028 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.287 | 1309.500 |
| % Hydrophobic | % Polar |
|---|---|
| 50.77 | 49.23 |
| According to VolSite | |
| HET Code: | IN0 |
|---|---|
| Formula: | C30H29ClN2O7 |
| Molecular weight: | 565.013 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.23 % |
| Polar Surface area: | 138.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -23.2281 | 67.8002 | 58.2435 |
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 |
| O65 | OG | SER- 51 | 3.16 | 158.15 | H-Bond (Protein Donor) |
| O65 | N | ARG- 52 | 3.15 | 127.66 | H-Bond (Protein Donor) |
| O66 | OG | SER- 53 | 3.12 | 156.83 | H-Bond (Protein Donor) |
| O66 | N | SER- 53 | 3.17 | 141.66 | H-Bond (Protein Donor) |
| C7 | CE2 | PHE- 54 | 4.29 | 0 | Hydrophobic |
| C28 | CZ | PHE- 54 | 3.39 | 0 | Hydrophobic |
| C14 | CD2 | PHE- 54 | 3.6 | 0 | Hydrophobic |
| O66 | N | PHE- 54 | 3.41 | 146.02 | H-Bond (Protein Donor) |
| CL36 | CD2 | PHE- 72 | 4.11 | 0 | Hydrophobic |
| CL36 | CD2 | TYR- 73 | 4.12 | 0 | Hydrophobic |
| C9 | CD2 | TYR- 73 | 3.32 | 0 | Hydrophobic |
| CL36 | CD1 | LEU- 76 | 3.94 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 76 | 3.85 | 0 | Hydrophobic |
| C32 | CB | ALA- 176 | 4 | 0 | Hydrophobic |
| CL36 | CG1 | VAL- 179 | 4.08 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 179 | 3.78 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 179 | 3.83 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 179 | 4.05 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 179 | 3.68 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 183 | 3.67 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 183 | 3.67 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 183 | 3.86 | 0 | Hydrophobic |
| C30 | CB | MET- 207 | 3.89 | 0 | Hydrophobic |
| C32 | CB | LEU- 211 | 3.88 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 211 | 3.74 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 211 | 3.64 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 211 | 3.54 | 0 | Hydrophobic |
| C27 | CE2 | PHE- 288 | 3.42 | 0 | Hydrophobic |
| C26 | SG | CYS- 289 | 4.1 | 0 | Hydrophobic |
| C28 | CG | PRO- 292 | 3.88 | 0 | Hydrophobic |
