sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2009-05-28
| 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: | 36.060 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.750 | 756.000 |
| % Hydrophobic | % Polar |
|---|---|
| 41.07 | 58.93 |
| According to VolSite | |
| HET Code: | QUD |
|---|---|
| Formula: | C29H37N4O2 |
| Molecular weight: | 473.630 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.01 % |
| Polar Surface area: | 81.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 25.9244 | 41.5757 | 42.7214 |
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 |
| C18 | CD2 | LEU- 30 | 3.38 | 0 | Hydrophobic |
| N31 | OD2 | ASP- 32 | 2.72 | 157.84 | H-Bond (Protein Donor) |
| N32 | OD1 | ASP- 32 | 2.77 | 159.33 | H-Bond (Ligand Donor) |
| C4 | CB | SER- 35 | 3.74 | 0 | Hydrophobic |
| C8 | CB | TYR- 71 | 4.28 | 0 | Hydrophobic |
| C11 | CB | TYR- 71 | 3.61 | 0 | Hydrophobic |
| C2 | CB | LYS- 75 | 4.4 | 0 | Hydrophobic |
| C16 | CE1 | PHE- 108 | 4.25 | 0 | Hydrophobic |
| C1 | CB | PHE- 108 | 4.22 | 0 | Hydrophobic |
| C16 | CH2 | TRP- 115 | 4.03 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 118 | 4.25 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 118 | 3.88 | 0 | Hydrophobic |
| C20 | CE1 | TYR- 198 | 3.64 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 226 | 3.82 | 0 | Hydrophobic |
| N32 | OD2 | ASP- 228 | 2.53 | 166.73 | H-Bond (Ligand Donor) |
| N33 | O | GLY- 230 | 3.21 | 165.53 | H-Bond (Ligand Donor) |
| C21 | CB | THR- 329 | 4.23 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 332 | 4.04 | 0 | Hydrophobic |
