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
2009-11-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.820 | 4.820 | 4.820 | 0.000 | 4.820 | 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: | 18.455 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.229 | 604.125 |
| % Hydrophobic | % Polar |
|---|---|
| 33.52 | 66.48 |
| According to VolSite | |
| HET Code: | G00 |
|---|---|
| Formula: | C12H18ClN2OS |
| Molecular weight: | 273.802 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.68 % |
| Polar Surface area: | 86.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 24.0476 | 10.7459 | 21.6421 |
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 |
| C7 | CD2 | LEU- 91 | 4.09 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 91 | 4.46 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 91 | 3.75 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 93 | 2.84 | 165.58 | H-Bond (Ligand Donor) |
| C11 | CB | SER- 96 | 3.84 | 0 | Hydrophobic |
| S1 | CE1 | TYR- 132 | 3.46 | 0 | Hydrophobic |
| CL1 | CD2 | TYR- 132 | 4.24 | 0 | Hydrophobic |
| C11 | CZ | TYR- 132 | 3.62 | 0 | Hydrophobic |
| CL1 | CG | GLN- 134 | 4.07 | 0 | Hydrophobic |
| CL1 | CD1 | PHE- 169 | 3.9 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 171 | 3.74 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 176 | 3.86 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 179 | 3.78 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 289 | 2.9 | 158.19 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 289 | 3.33 | 130.87 | H-Bond (Ligand Donor) |
