sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.960 Å
X-ray
2012-09-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.520 | 8.520 | 8.520 | 0.000 | 8.520 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 26.303 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.157 | 1161.000 |
| % Hydrophobic | % Polar |
|---|---|
| 29.94 | 70.06 |
| According to VolSite | |
| HET Code: | 10V |
|---|---|
| Formula: | C24H23N6O2S |
| Molecular weight: | 459.543 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.32 % |
| Polar Surface area: | 135.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 21.0856 | 34.6829 | 56.4324 |
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 |
| C5 | CD2 | LEU- 91 | 3.69 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 93 | 3.5 | 128.89 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 93 | 2.79 | 169.06 | H-Bond (Ligand Donor) |
| C15 | CB | SER- 96 | 3.91 | 0 | Hydrophobic |
| C20 | CB | SER- 96 | 3.68 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 130 | 3.85 | 0 | Hydrophobic |
| C12 | CD2 | TYR- 132 | 3.97 | 0 | Hydrophobic |
| C18 | CB | TYR- 132 | 4.19 | 0 | Hydrophobic |
| S1 | CZ | TYR- 132 | 3.49 | 0 | Hydrophobic |
| S1 | CD1 | ILE- 179 | 4.46 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 179 | 4.07 | 0 | Hydrophobic |
| C24 | CG | ARG- 189 | 3.38 | 0 | Hydrophobic |
| C25 | CE1 | TYR- 259 | 4.22 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 289 | 2.73 | 156.51 | H-Bond (Ligand Donor) |
