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
2012-08-16
| 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: | 19.224 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.934 | 1066.500 |
| % Hydrophobic | % Polar |
|---|---|
| 30.38 | 69.62 |
| According to VolSite | |
| HET Code: | 54M |
|---|---|
| Formula: | C21H21N4O |
| Molecular weight: | 345.418 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.08 % |
| Polar Surface area: | 75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 5.36504 | 1.50915 | -21.1053 |
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 | 4.49 | 0 | Hydrophobic |
| N20 | OD1 | ASP- 32 | 2.76 | 173.83 | H-Bond (Ligand Donor) |
| N20 | OD2 | ASP- 32 | 3.42 | 122.22 | H-Bond (Ligand Donor) |
| C1 | CB | SER- 35 | 3.52 | 0 | Hydrophobic |
| C15 | CB | ASN- 37 | 4.1 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 69 | 4.23 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 69 | 4.35 | 0 | Hydrophobic |
| C19 | CE2 | TYR- 71 | 4.11 | 0 | Hydrophobic |
| C3 | CB | TYR- 71 | 4.26 | 0 | Hydrophobic |
| C15 | CZ2 | TRP- 76 | 3.67 | 0 | Hydrophobic |
| O14 | NE1 | TRP- 76 | 3.02 | 169.86 | H-Bond (Protein Donor) |
| C6 | CD1 | ILE- 118 | 3.74 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 118 | 3.47 | 0 | Hydrophobic |
| C15 | CG | ARG- 128 | 4.44 | 0 | Hydrophobic |
| N20 | OD2 | ASP- 228 | 2.9 | 162.69 | H-Bond (Ligand Donor) |
