sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2007-12-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.750 | 8.750 | 8.750 | 0.000 | 8.750 | 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: | 25.595 |
|---|---|
| Number of residues: | 56 |
| Including | |
| Standard Amino Acids: | 48 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 8 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.942 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 38.19 | 61.81 |
| According to VolSite | |
| HET Code: | BSD |
|---|---|
| Formula: | C36H43N4O6S |
| Molecular weight: | 659.815 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.34 % |
| Polar Surface area: | 150.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 34.8934 | -6.964 | 75.8368 |
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 | CD1 | LEU- 30 | 4.1 | 0 | Hydrophobic |
| C38 | CD2 | LEU- 30 | 3.44 | 0 | Hydrophobic |
| O3 | OD2 | ASP- 32 | 2.7 | 147.35 | H-Bond (Ligand Donor) |
| C48 | CB | SER- 35 | 3.84 | 0 | Hydrophobic |
| C48 | CG1 | VAL- 69 | 3.61 | 0 | Hydrophobic |
| C32 | CD1 | TYR- 71 | 3.67 | 0 | Hydrophobic |
| C34 | CB | TYR- 71 | 3.99 | 0 | Hydrophobic |
| C39 | CD1 | TYR- 71 | 4.03 | 0 | Hydrophobic |
| C48 | CD1 | TYR- 71 | 3.58 | 0 | Hydrophobic |
| C26 | CB | THR- 72 | 4.33 | 0 | Hydrophobic |
| C29 | CG2 | THR- 72 | 3.74 | 0 | Hydrophobic |
| O21 | NE2 | GLN- 73 | 3.22 | 135.51 | H-Bond (Protein Donor) |
| O22 | N | GLN- 73 | 3.03 | 161.25 | H-Bond (Protein Donor) |
| C26 | CB | GLN- 73 | 3.55 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 110 | 3.72 | 0 | Hydrophobic |
| C18 | CZ2 | TRP- 115 | 4.19 | 0 | Hydrophobic |
| C38 | CD1 | ILE- 118 | 3.77 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 228 | 3.01 | 0 | Ionic (Ligand Cationic) |
| N21 | O | GLY- 230 | 3.16 | 169.6 | H-Bond (Ligand Donor) |
| N3 | O | GLY- 230 | 3.07 | 154.62 | H-Bond (Ligand Donor) |
| C27 | CB | THR- 231 | 4.39 | 0 | Hydrophobic |
| C29 | CG2 | THR- 231 | 4.4 | 0 | Hydrophobic |
| C25 | CG2 | THR- 231 | 3.99 | 0 | Hydrophobic |
| C11 | CB | THR- 232 | 4.12 | 0 | Hydrophobic |
| C12 | CG2 | THR- 232 | 3.95 | 0 | Hydrophobic |
| O24 | N | ASN- 233 | 2.95 | 169.8 | H-Bond (Protein Donor) |
| C29 | CD | ARG- 235 | 3.58 | 0 | Hydrophobic |
| C13 | CB | ALA- 335 | 3.48 | 0 | Hydrophobic |
