sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2011-05-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.220 | 5.220 | 5.220 | 0.000 | 5.220 | 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: | 43.316 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.596 | 806.625 |
| % Hydrophobic | % Polar |
|---|---|
| 40.17 | 59.83 |
| According to VolSite | |
| HET Code: | RTH |
|---|---|
| Formula: | C21H20N2 |
| Molecular weight: | 300.397 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.69 % |
| Polar Surface area: | 38.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 70.1519 | 49.2892 | 9.67417 |
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 |
| C21 | CD2 | LEU- 30 | 4.4 | 0 | Hydrophobic |
| N17 | OD1 | ASP- 32 | 2.82 | 161.47 | H-Bond (Ligand Donor) |
| N7 | OD1 | ASP- 32 | 3.5 | 129.94 | H-Bond (Ligand Donor) |
| N7 | OD2 | ASP- 32 | 2.65 | 167.43 | H-Bond (Ligand Donor) |
| C3 | CB | SER- 35 | 4.34 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 69 | 3.98 | 0 | Hydrophobic |
| C15 | CB | TYR- 71 | 3.46 | 0 | Hydrophobic |
| C18 | CD1 | PHE- 108 | 3.92 | 0 | Hydrophobic |
| C13 | CB | PHE- 108 | 4.01 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 110 | 4.41 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 118 | 3.24 | 0 | Hydrophobic |
| N17 | OD2 | ASP- 228 | 2.99 | 159.49 | H-Bond (Ligand Donor) |
