sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.740 Å
X-ray
2012-06-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.570 | 6.570 | 6.570 | 0.000 | 6.570 | 1 |
| 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: | 26.023 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.983 | 978.750 |
| % Hydrophobic | % Polar |
|---|---|
| 29.31 | 70.69 |
| According to VolSite | |
| HET Code: | H24 |
|---|---|
| Formula: | C19H22N3O2 |
| Molecular weight: | 324.397 g/mol |
| DrugBank ID: | DB07874 |
| Buried Surface Area: | 63.7 % |
| Polar Surface area: | 69.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 25.2681 | 10.574 | 21.4812 |
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 |
| C3 | CD1 | LEU- 91 | 4.36 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 91 | 3.9 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 91 | 3.9 | 0 | Hydrophobic |
| N24 | OD1 | ASP- 93 | 2.77 | 173.65 | H-Bond (Ligand Donor) |
| N24 | OD2 | ASP- 93 | 3.42 | 124.99 | H-Bond (Ligand Donor) |
| C15 | CZ | TYR- 132 | 3.61 | 0 | Hydrophobic |
| C18 | CE1 | TYR- 132 | 3.51 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 169 | 4.43 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 171 | 4.14 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 171 | 3.45 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 179 | 3.68 | 0 | Hydrophobic |
| N24 | OD2 | ASP- 289 | 2.91 | 159.22 | H-Bond (Ligand Donor) |
| C1 | CB | ALA- 396 | 3.96 | 0 | Hydrophobic |
