sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2011-09-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.630 | 6.630 | 6.630 | 0.000 | 6.630 | 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: | 39.069 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.705 | 870.750 |
| % Hydrophobic | % Polar |
|---|---|
| 38.37 | 61.63 |
| According to VolSite | |
| HET Code: | 5HA |
|---|---|
| Formula: | C31H39N4O5S |
| Molecular weight: | 579.730 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.3 % |
| Polar Surface area: | 140.79 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 69.9505 | 46.0948 | 6.34159 |
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 |
| C28 | CD2 | LEU- 30 | 3.73 | 0 | Hydrophobic |
| O3 | OD1 | ASP- 32 | 3.3 | 139.05 | H-Bond (Ligand Donor) |
| O3 | OD2 | ASP- 32 | 2.67 | 161.44 | H-Bond (Ligand Donor) |
| N1 | O | GLY- 34 | 3.14 | 140.9 | H-Bond (Ligand Donor) |
| C8 | CZ | TYR- 71 | 4.49 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 110 | 4.37 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 118 | 3.72 | 0 | Hydrophobic |
| C1 | CE1 | TYR- 198 | 3.4 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 226 | 3.83 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 228 | 2.92 | 149.43 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 228 | 2.92 | 0 | Ionic (Ligand Cationic) |
| N2 | O | GLY- 230 | 2.86 | 162.81 | H-Bond (Ligand Donor) |
| N4 | O | GLY- 230 | 3.4 | 150.79 | H-Bond (Ligand Donor) |
| C13 | CG2 | THR- 231 | 4 | 0 | Hydrophobic |
| C30 | CB | THR- 232 | 4.48 | 0 | Hydrophobic |
| C34 | CG2 | THR- 232 | 4.03 | 0 | Hydrophobic |
| O5 | ND2 | ASN- 233 | 3.15 | 128.92 | H-Bond (Protein Donor) |
| O6 | N | ASN- 233 | 3.11 | 139.91 | H-Bond (Protein Donor) |
| C16 | CD | ARG- 235 | 4.31 | 0 | Hydrophobic |
| C33 | CB | ALA- 335 | 3.85 | 0 | Hydrophobic |
