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
2013-05-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.570 | 4.570 | 4.570 | 0.000 | 4.570 | 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: | 39.606 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.264 | 577.125 |
| % Hydrophobic | % Polar |
|---|---|
| 32.75 | 67.25 |
| According to VolSite | |
| HET Code: | 0B4 |
|---|---|
| Formula: | C15H20N3O |
| Molecular weight: | 258.339 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.27 % |
| Polar Surface area: | 60.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 19.5702 | 39.1253 | -7.58642 |
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 |
| C9 | CD2 | LEU- 30 | 3.71 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 32 | 2.92 | 153.98 | H-Bond (Ligand Donor) |
| C1 | CB | SER- 35 | 3.86 | 0 | Hydrophobic |
| C6 | CZ | TYR- 71 | 3.81 | 0 | Hydrophobic |
| C1 | CZ | TYR- 71 | 3.64 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 108 | 4.26 | 0 | Hydrophobic |
| C7 | CE1 | PHE- 108 | 3.56 | 0 | Hydrophobic |
| C9 | CZ | PHE- 108 | 3.88 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 110 | 4.02 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 118 | 3.72 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 228 | 2.78 | 152.46 | H-Bond (Ligand Donor) |
