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
2013-03-18
| 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: | 22.948 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.414 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 34.81 | 65.19 |
| According to VolSite | |
| HET Code: | 8T3 |
|---|---|
| Formula: | C19H19ClFN4O |
| Molecular weight: | 373.832 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.74 % |
| Polar Surface area: | 81.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -18.825 | 40.6264 | 92.0881 |
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 |
| CL | CE1 | TYR- 75 | 4.24 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 91 | 4.29 | 0 | Hydrophobic |
| N17 | OD2 | ASP- 93 | 3.39 | 128.67 | H-Bond (Ligand Donor) |
| N17 | OD1 | ASP- 93 | 2.72 | 171.96 | H-Bond (Ligand Donor) |
| C24 | CB | SER- 96 | 4.16 | 0 | Hydrophobic |
| F23 | CE2 | TYR- 132 | 3.26 | 0 | Hydrophobic |
| C24 | CZ | TYR- 132 | 3.63 | 0 | Hydrophobic |
| C9 | CE1 | TYR- 132 | 3.7 | 0 | Hydrophobic |
| C4 | CD1 | TYR- 132 | 4.41 | 0 | Hydrophobic |
| F23 | CD1 | PHE- 169 | 3.43 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 179 | 4.04 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 179 | 3.83 | 0 | Hydrophobic |
| N17 | OD2 | ASP- 289 | 2.83 | 163.5 | H-Bond (Ligand Donor) |
| N11 | O | GLY- 291 | 2.9 | 132.74 | H-Bond (Ligand Donor) |
| C25 | CB | THR- 293 | 4.39 | 0 | Hydrophobic |
| CL | CB | THR- 293 | 4.23 | 0 | Hydrophobic |
| CL | CB | ALA- 396 | 3.47 | 0 | Hydrophobic |
