sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2012-02-22
| 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: | 28.096 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.520 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 36.73 | 63.27 |
| According to VolSite | |
| HET Code: | 0MP |
|---|---|
| Formula: | C28H39FN3O3 |
| Molecular weight: | 484.626 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.74 % |
| Polar Surface area: | 88.06 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 66.1689 | 47.9865 | 9.20074 |
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 |
| C21 | CD1 | LEU- 30 | 3.82 | 0 | Hydrophobic |
| O30 | OD1 | ASP- 32 | 3.28 | 135.95 | H-Bond (Ligand Donor) |
| O30 | OD2 | ASP- 32 | 2.62 | 157.56 | H-Bond (Ligand Donor) |
| N29 | O | GLY- 34 | 3.05 | 138.71 | H-Bond (Ligand Donor) |
| C18 | CB | SER- 35 | 4.15 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 69 | 3.79 | 0 | Hydrophobic |
| C14 | CD1 | TYR- 71 | 3.61 | 0 | Hydrophobic |
| C26 | CD1 | TYR- 71 | 4.19 | 0 | Hydrophobic |
| C31 | CD1 | TYR- 71 | 3.94 | 0 | Hydrophobic |
| C24 | CB | TYR- 71 | 3.98 | 0 | Hydrophobic |
| C35 | CB | THR- 72 | 4.33 | 0 | Hydrophobic |
| O34 | N | THR- 72 | 3.19 | 150.84 | H-Bond (Protein Donor) |
| F32 | CD1 | ILE- 110 | 3.98 | 0 | Hydrophobic |
| F32 | CZ2 | TRP- 115 | 3.71 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 118 | 3.66 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 126 | 3.97 | 0 | Hydrophobic |
| C16 | CD | ARG- 128 | 3.67 | 0 | Hydrophobic |
| C2 | CZ | TYR- 198 | 3.93 | 0 | Hydrophobic |
| C18 | CE1 | TYR- 198 | 4.28 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 226 | 4.23 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 226 | 3.96 | 0 | Hydrophobic |
| N29 | OD2 | ASP- 228 | 2.52 | 169.55 | H-Bond (Ligand Donor) |
| N29 | OD2 | ASP- 228 | 2.52 | 0 | Ionic (Ligand Cationic) |
| N27 | O | GLY- 230 | 2.69 | 169.85 | H-Bond (Ligand Donor) |
| C3 | CB | THR- 329 | 3.79 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 332 | 3.6 | 0 | Hydrophobic |
