sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2012-09-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.050 | 7.050 | 7.050 | 0.000 | 7.050 | 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: | 16.394 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.942 | 1076.625 |
| % Hydrophobic | % Polar |
|---|---|
| 32.29 | 67.71 |
| According to VolSite | |
| HET Code: | 10W |
|---|---|
| Formula: | C24H21FN5OS |
| Molecular weight: | 446.520 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.96 % |
| Polar Surface area: | 113.19 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 |
|---|---|---|
| 20.4543 | 34.7339 | 55.5834 |
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 |
| F1 | CB | GLN- 73 | 4.43 | 0 | Hydrophobic |
| S1 | CD2 | LEU- 91 | 4.1 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 91 | 4.06 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 93 | 3.47 | 127.59 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 93 | 2.82 | 165.96 | H-Bond (Ligand Donor) |
| C6 | CB | SER- 96 | 4.19 | 0 | Hydrophobic |
| C20 | CB | SER- 96 | 3.51 | 0 | Hydrophobic |
| C21 | CB | ASN- 98 | 4.25 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 130 | 3.58 | 0 | Hydrophobic |
| C4 | CE2 | TYR- 132 | 3.73 | 0 | Hydrophobic |
| C7 | CG | TYR- 132 | 3.95 | 0 | Hydrophobic |
| C16 | CG1 | ILE- 171 | 3.99 | 0 | Hydrophobic |
| C17 | CZ2 | TRP- 176 | 3.49 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 179 | 3.6 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 179 | 4.03 | 0 | Hydrophobic |
| C22 | CG | ARG- 189 | 3.56 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 289 | 2.87 | 155.55 | H-Bond (Ligand Donor) |
