sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 Å
X-ray
2012-02-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.270 | 8.270 | 8.270 | 0.000 | 8.270 | 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: | 21.878 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.967 | 1026.000 |
| % Hydrophobic | % Polar |
|---|---|
| 28.95 | 71.05 |
| According to VolSite | |
| HET Code: | 0KR |
|---|---|
| Formula: | C21H21N4O |
| Molecular weight: | 345.418 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.06 % |
| 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: | 4 |
| X | Y | Z |
|---|---|---|
| 18.4477 | 34.6128 | 55.9859 |
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 |
| C23 | CD1 | TYR- 75 | 4.49 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 91 | 3.98 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 91 | 3.94 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 93 | 2.68 | 151.74 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 93 | 3.46 | 120.98 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 93 | 2.81 | 166.13 | H-Bond (Ligand Donor) |
| C2 | OD2 | ASP- 93 | 3.5 | 0 | Ionic (Ligand Cationic) |
| C2 | OD1 | ASP- 93 | 3.52 | 0 | Ionic (Ligand Cationic) |
| C13 | CB | SER- 96 | 3.65 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 179 | 4.4 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 179 | 4.44 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 179 | 3.57 | 0 | Hydrophobic |
| C2 | OD2 | ASP- 289 | 3.86 | 0 | Ionic (Ligand Cationic) |
| N3 | OD2 | ASP- 289 | 2.79 | 153.6 | H-Bond (Ligand Donor) |
| C23 | CB | ALA- 396 | 3.53 | 0 | Hydrophobic |
