sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2013-06-13
| 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: | 31.458 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.087 | 1265.625 |
| % Hydrophobic | % Polar |
|---|---|
| 31.47 | 68.53 |
| According to VolSite | |
| HET Code: | 1W2 |
|---|---|
| Formula: | C18H16F2N5O |
| Molecular weight: | 356.349 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.42 % |
| Polar Surface area: | 89.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 14.9328 | -7.82162 | 17.1608 |
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 | CD2 | LEU- 30 | 3.54 | 0 | Hydrophobic |
| N16 | OD1 | ASP- 32 | 2.67 | 161.98 | H-Bond (Ligand Donor) |
| N16 | OD2 | ASP- 32 | 3.34 | 128.18 | H-Bond (Ligand Donor) |
| C2 | CB | SER- 35 | 3.43 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 69 | 4.13 | 0 | Hydrophobic |
| C8 | CB | TYR- 71 | 4.39 | 0 | Hydrophobic |
| C9 | CD1 | TYR- 71 | 4.03 | 0 | Hydrophobic |
| C12 | CG | TYR- 71 | 4.46 | 0 | Hydrophobic |
| F23 | CD1 | TYR- 71 | 3.32 | 0 | Hydrophobic |
| N26 | NE1 | TRP- 76 | 3.19 | 156.05 | H-Bond (Protein Donor) |
| F24 | CD1 | PHE- 108 | 4.17 | 0 | Hydrophobic |
| F24 | CD1 | ILE- 110 | 3.87 | 0 | Hydrophobic |
| F24 | CZ2 | TRP- 115 | 3.3 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 118 | 3.81 | 0 | Hydrophobic |
| N16 | OD2 | ASP- 228 | 2.81 | 170.59 | H-Bond (Ligand Donor) |
