sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-11-20
| 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: | 36.078 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.783 | 951.750 |
| % Hydrophobic | % Polar |
|---|---|
| 29.79 | 70.21 |
| According to VolSite | |
| HET Code: | 1BE |
|---|---|
| Formula: | C24H27ClN4O2S |
| Molecular weight: | 471.015 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.26 % |
| Polar Surface area: | 123.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 9.68572 | -16.2962 | 8.30506 |
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 |
| C28 | CD2 | LEU- 91 | 3.95 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 91 | 3.71 | 0 | Hydrophobic |
| S17 | CD2 | LEU- 91 | 4.09 | 0 | Hydrophobic |
| CL1 | CD2 | TYR- 132 | 3.72 | 0 | Hydrophobic |
| C9 | CE1 | TYR- 132 | 3.65 | 0 | Hydrophobic |
| C1 | CB | TYR- 132 | 4.17 | 0 | Hydrophobic |
| C6 | CB | GLN- 134 | 4.01 | 0 | Hydrophobic |
| N26 | O | LYS- 168 | 2.75 | 164.98 | H-Bond (Ligand Donor) |
| CL1 | CD1 | PHE- 169 | 3.87 | 0 | Hydrophobic |
| C27 | CE1 | PHE- 169 | 4.13 | 0 | Hydrophobic |
| C9 | CE1 | PHE- 169 | 4.17 | 0 | Hydrophobic |
| C2 | CD1 | PHE- 169 | 3.43 | 0 | Hydrophobic |
| C27 | CH2 | TRP- 176 | 4.46 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 179 | 3.83 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 179 | 4.31 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 179 | 4.48 | 0 | Hydrophobic |
| O8 | N | THR- 293 | 2.74 | 168.67 | H-Bond (Protein Donor) |
| C19 | CB | THR- 293 | 4.47 | 0 | Hydrophobic |
| C21 | CB | ALA- 396 | 3.61 | 0 | Hydrophobic |
