sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-06-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.770 | 8.770 | 8.770 | 0.000 | 8.770 | 2 |
| 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: | 25.361 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.577 | 685.125 |
| % Hydrophobic | % Polar |
|---|---|
| 34.98 | 65.02 |
| According to VolSite | |
| HET Code: | 0V6 |
|---|---|
| Formula: | C18H18ClN4OS |
| Molecular weight: | 373.880 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.83 % |
| Polar Surface area: | 99.06 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| 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 |
|---|---|---|
| 24.7602 | 10.6367 | 21.619 |
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 |
| S1 | CD2 | LEU- 91 | 4.01 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 91 | 3.74 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 91 | 4.38 | 0 | Hydrophobic |
| N10 | OD2 | ASP- 93 | 2.63 | 145.06 | H-Bond (Protein Donor) |
| N20 | OD2 | ASP- 93 | 3.49 | 126.21 | H-Bond (Ligand Donor) |
| N20 | OD1 | ASP- 93 | 2.8 | 160.17 | H-Bond (Ligand Donor) |
| C12 | CB | SER- 96 | 3.91 | 0 | Hydrophobic |
| C6 | CE1 | TYR- 132 | 3.51 | 0 | Hydrophobic |
| C12 | CZ | TYR- 132 | 3.5 | 0 | Hydrophobic |
| CL | CD2 | TYR- 132 | 3.42 | 0 | Hydrophobic |
| CL | CB | GLN- 134 | 3.7 | 0 | Hydrophobic |
| CL | CD1 | PHE- 169 | 3.63 | 0 | Hydrophobic |
| S1 | CD1 | ILE- 179 | 4.15 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 179 | 4.24 | 0 | Hydrophobic |
| N20 | OD2 | ASP- 289 | 2.81 | 158.28 | H-Bond (Ligand Donor) |
| C25 | CB | ALA- 396 | 3.56 | 0 | Hydrophobic |
