sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-09-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.000 | 9.000 | 9.000 | 0.000 | 9.000 | 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: | 18.189 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.036 | 1140.750 |
| % Hydrophobic | % Polar |
|---|---|
| 31.95 | 68.05 |
| According to VolSite | |
| HET Code: | 10O |
|---|---|
| Formula: | C24H23N6O2S |
| Molecular weight: | 459.543 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.28 % |
| Polar Surface area: | 135.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 20.4142 | 34.9455 | 55.4014 |
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 |
| C14 | CD2 | LEU- 91 | 4.33 | 0 | Hydrophobic |
| N5 | OD2 | ASP- 93 | 3.45 | 128.46 | H-Bond (Ligand Donor) |
| N5 | OD1 | ASP- 93 | 2.78 | 171.25 | H-Bond (Ligand Donor) |
| C24 | CB | SER- 96 | 4.43 | 0 | Hydrophobic |
| C23 | CB | SER- 96 | 3.79 | 0 | Hydrophobic |
| C23 | CB | ASN- 98 | 4.11 | 0 | Hydrophobic |
| C24 | CB | ASN- 98 | 4.08 | 0 | Hydrophobic |
| C24 | CB | ALA- 100 | 3.84 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 130 | 3.58 | 0 | Hydrophobic |
| C2 | CE2 | TYR- 132 | 3.73 | 0 | Hydrophobic |
| C7 | CG | TYR- 132 | 3.85 | 0 | Hydrophobic |
| C24 | CZ2 | TRP- 137 | 4.35 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 169 | 4.33 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 171 | 3.3 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 179 | 3.67 | 0 | Hydrophobic |
| S1 | CD1 | ILE- 179 | 3.62 | 0 | Hydrophobic |
| C24 | CB | ILE- 179 | 3.7 | 0 | Hydrophobic |
| C22 | CG | ARG- 189 | 4.16 | 0 | Hydrophobic |
| N5 | OD2 | ASP- 289 | 2.87 | 159.71 | H-Bond (Ligand Donor) |
