sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-06-26
| 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: | 26.154 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.134 | 1350.000 |
| % Hydrophobic | % Polar |
|---|---|
| 37.00 | 63.00 |
| According to VolSite | |
| HET Code: | DWD |
|---|---|
| Formula: | C23H23N4O3 |
| Molecular weight: | 403.454 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.11 % |
| Polar Surface area: | 93.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 69.2467 | 49.488 | 8.4613 |
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 |
| C2 | CD2 | LEU- 30 | 3.67 | 0 | Hydrophobic |
| N21 | OD1 | ASP- 32 | 2.68 | 152.41 | H-Bond (Ligand Donor) |
| N21 | OD2 | ASP- 32 | 3.42 | 123.03 | H-Bond (Ligand Donor) |
| C22 | CB | SER- 35 | 4.33 | 0 | Hydrophobic |
| C24 | CB | SER- 35 | 4.26 | 0 | Hydrophobic |
| C13 | CB | SER- 35 | 3.94 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 69 | 4.1 | 0 | Hydrophobic |
| C22 | CB | TYR- 71 | 4.23 | 0 | Hydrophobic |
| C17 | CD1 | TYR- 71 | 3.91 | 0 | Hydrophobic |
| C13 | CB | TYR- 71 | 3.89 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 71 | 3.81 | 0 | Aromatic Face/Face |
| C4 | CD1 | ILE- 118 | 3.93 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 118 | 3.86 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 126 | 4.04 | 0 | Hydrophobic |
| C24 | CE1 | TYR- 198 | 4.49 | 0 | Hydrophobic |
| N21 | OD2 | ASP- 228 | 2.84 | 155.79 | H-Bond (Ligand Donor) |
