sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.760 Å
X-ray
2011-05-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.420 | 4.420 | 4.420 | 0.000 | 4.420 | 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: | 44.343 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.580 | 631.125 |
| % Hydrophobic | % Polar |
|---|---|
| 39.04 | 60.96 |
| According to VolSite | |
| HET Code: | RTM |
|---|---|
| Formula: | C19H25N3O |
| Molecular weight: | 311.421 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 43.8 % |
| Polar Surface area: | 59.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 69.0643 | 48.5898 | 8.244 |
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 |
| C17 | CD2 | LEU- 30 | 4.44 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 30 | 4.46 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 32 | 2.67 | 173.91 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 32 | 2.76 | 176.42 | H-Bond (Ligand Donor) |
| C3 | CB | SER- 35 | 3.57 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 69 | 4.41 | 0 | Hydrophobic |
| C4 | CB | TYR- 71 | 4.24 | 0 | Hydrophobic |
| C16 | CE1 | PHE- 108 | 4.09 | 0 | Hydrophobic |
| C17 | CH2 | TRP- 115 | 4.03 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 118 | 4.01 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 118 | 3.48 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 228 | 2.85 | 145.76 | H-Bond (Ligand Donor) |
