sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2012-02-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.680 | 7.680 | 7.680 | 0.000 | 7.680 | 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: | 17.210 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.967 | 1056.375 |
| % Hydrophobic | % Polar |
|---|---|
| 29.71 | 70.29 |
| According to VolSite | |
| HET Code: | 0KQ |
|---|---|
| Formula: | C18H18ClN4O |
| Molecular weight: | 341.815 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.69 % |
| Polar Surface area: | 70.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 18.8002 | 34.5513 | 55.9081 |
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 |
| C10 | CD2 | LEU- 91 | 3.9 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 91 | 3.96 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 93 | 2.65 | 151.75 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 93 | 2.77 | 166.78 | H-Bond (Ligand Donor) |
| C3 | OD2 | ASP- 93 | 3.44 | 0 | Ionic (Ligand Cationic) |
| C3 | OD1 | ASP- 93 | 3.5 | 0 | Ionic (Ligand Cationic) |
| C17 | CB | SER- 96 | 3.81 | 0 | Hydrophobic |
| C6 | CE2 | TYR- 132 | 4.29 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 179 | 4.4 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 179 | 4.46 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 179 | 3.46 | 0 | Hydrophobic |
| C3 | OD2 | ASP- 289 | 3.88 | 0 | Ionic (Ligand Cationic) |
| N3 | OD2 | ASP- 289 | 2.83 | 154.53 | H-Bond (Ligand Donor) |
