sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2011-10-28
| 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: | 30.993 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.820 | 955.125 |
| % Hydrophobic | % Polar |
|---|---|
| 31.10 | 68.90 |
| According to VolSite | |
| HET Code: | 092 |
|---|---|
| Formula: | C13H15N2O3 |
| Molecular weight: | 247.270 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.09 % |
| Polar Surface area: | 72.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 22.9245 | 37.0234 | 42.1938 |
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 |
| C5 | CD2 | LEU- 30 | 3.55 | 0 | Hydrophobic |
| N10 | OD1 | ASP- 32 | 2.83 | 151.21 | H-Bond (Ligand Donor) |
| N10 | OD2 | ASP- 32 | 3.22 | 130.81 | H-Bond (Ligand Donor) |
| N10 | OD1 | ASP- 32 | 2.83 | 0 | Ionic (Ligand Cationic) |
| N10 | OD2 | ASP- 32 | 3.22 | 0 | Ionic (Ligand Cationic) |
| C4 | CB | SER- 35 | 4.49 | 0 | Hydrophobic |
| C4 | CE1 | TYR- 71 | 3.64 | 0 | Hydrophobic |
| C18 | CD1 | TYR- 71 | 4.45 | 0 | Hydrophobic |
| N16 | O | GLN- 73 | 3.42 | 162.77 | H-Bond (Ligand Donor) |
| C3 | CD1 | ILE- 118 | 4.03 | 0 | Hydrophobic |
| C18 | CE1 | TYR- 198 | 4.13 | 0 | Hydrophobic |
| N10 | OD2 | ASP- 228 | 2.86 | 147.37 | H-Bond (Ligand Donor) |
| N10 | OD2 | ASP- 228 | 2.86 | 0 | Ionic (Ligand Cationic) |
| N10 | OD1 | ASP- 228 | 3.47 | 0 | Ionic (Ligand Cationic) |
