sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2012-08-16
| 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: | 21.847 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.041 | 1113.750 |
| % Hydrophobic | % Polar |
|---|---|
| 26.67 | 73.33 |
| According to VolSite | |
| HET Code: | WM9 |
|---|---|
| Formula: | C17H18ClN2O |
| Molecular weight: | 301.791 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.72 % |
| Polar Surface area: | 49.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 4.918 | -0.0369048 | -19.7533 |
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 |
| C19 | CD1 | LEU- 30 | 4.48 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 30 | 3.89 | 0 | Hydrophobic |
| N8 | OD2 | ASP- 32 | 3.41 | 122.9 | H-Bond (Ligand Donor) |
| N8 | OD1 | ASP- 32 | 2.72 | 176.04 | H-Bond (Ligand Donor) |
| C1 | CB | SER- 35 | 4.22 | 0 | Hydrophobic |
| C1 | CE1 | TYR- 71 | 3.53 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 110 | 3.57 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 118 | 3.92 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 118 | 3.56 | 0 | Hydrophobic |
| N8 | OD2 | ASP- 228 | 2.82 | 163.31 | H-Bond (Ligand Donor) |
