sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2007-01-02
| Name: | Beta-secretase 1 |
|---|---|
| ID: | BACE1_HUMAN |
| AC: | P56817 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.23.46 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 36.369 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.274 | 614.250 |
| % Hydrophobic | % Polar |
|---|---|
| 33.52 | 66.48 |
| According to VolSite | |
| HET Code: | CMZ |
|---|---|
| Formula: | C15H24NO3 |
| Molecular weight: | 266.356 g/mol |
| DrugBank ID: | DB07573 |
| Buried Surface Area: | 49.58 % |
| Polar Surface area: | 43.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 68.0275 | 47.8215 | 8.51784 |
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 |
| C1 | CD2 | LEU- 30 | 3.68 | 0 | Hydrophobic |
| O11 | OD1 | ASP- 32 | 2.56 | 127.87 | H-Bond (Ligand Donor) |
| O11 | OD2 | ASP- 32 | 2.89 | 161.38 | H-Bond (Ligand Donor) |
| C6 | CG | TYR- 71 | 3.58 | 0 | Hydrophobic |
| C3 | CD1 | PHE- 108 | 3.46 | 0 | Hydrophobic |
| C1 | CH2 | TRP- 115 | 3.47 | 0 | Hydrophobic |
| C17 | CE1 | TYR- 198 | 3.8 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 226 | 4.15 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 226 | 3.64 | 0 | Hydrophobic |
| N13 | OD2 | ASP- 228 | 2.89 | 153.39 | H-Bond (Ligand Donor) |
| N13 | OD2 | ASP- 228 | 2.89 | 0 | Ionic (Ligand Cationic) |
| C15 | CG2 | VAL- 332 | 3.78 | 0 | Hydrophobic |
