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
2007-01-10
| 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: | 25.084 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.976 | 897.750 |
| % Hydrophobic | % Polar |
|---|---|
| 44.74 | 55.26 |
| According to VolSite | |
| HET Code: | 8IP |
|---|---|
| Formula: | C17H16N4 |
| Molecular weight: | 276.336 g/mol |
| DrugBank ID: | DB07284 |
| Buried Surface Area: | 51.08 % |
| Polar Surface area: | 63.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 69.5058 | 46.8438 | 7.13429 |
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 |
| C16 | CD2 | LEU- 30 | 4.11 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 30 | 3.89 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 32 | 2.84 | 122.3 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 32 | 3.18 | 175.14 | H-Bond (Ligand Donor) |
| N8 | OD2 | ASP- 32 | 2.93 | 164.93 | H-Bond (Ligand Donor) |
| C9 | CZ | TYR- 71 | 4.35 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 110 | 3.82 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 118 | 3.75 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 228 | 2.87 | 144.84 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 228 | 3.19 | 133.58 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 228 | 2.69 | 160.59 | H-Bond (Ligand Donor) |
