sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-09-10
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 36.699 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.013 | 985.500 |
| % Hydrophobic | % Polar |
|---|---|
| 36.30 | 63.70 |
| According to VolSite | |
| HET Code: | 10J |
|---|---|
| Formula: | C25H22N5O2S |
| Molecular weight: | 456.539 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.4 % |
| Polar Surface area: | 130.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 21.9498 | 10.664 | 21.6411 |
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 |
| C18 | CD2 | LEU- 91 | 3.61 | 0 | Hydrophobic |
| N21 | OD2 | ASP- 93 | 3.35 | 128.85 | H-Bond (Ligand Donor) |
| N21 | OD1 | ASP- 93 | 2.69 | 167.13 | H-Bond (Ligand Donor) |
| C26 | CB | SER- 96 | 3.7 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 130 | 3.54 | 0 | Hydrophobic |
| C2 | CD2 | TYR- 132 | 3.85 | 0 | Hydrophobic |
| S14 | CZ | TYR- 132 | 3.3 | 0 | Hydrophobic |
| C28 | CZ2 | TRP- 176 | 3.43 | 0 | Hydrophobic |
| S14 | CD1 | ILE- 179 | 4.21 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 187 | 4.05 | 0 | Hydrophobic |
| C32 | CD | ARG- 189 | 3.82 | 0 | Hydrophobic |
| N21 | OD2 | ASP- 289 | 2.85 | 160.57 | H-Bond (Ligand Donor) |
