sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2007-03-21
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 39.223 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.278 | 1080.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.50 | 57.50 |
| According to VolSite | |
| HET Code: | MR0 |
|---|---|
| Formula: | C33H41F2N4O5 |
| Molecular weight: | 611.699 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.94 % |
| Polar Surface area: | 138.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 16 |
| X | Y | Z |
|---|---|---|
| -44.1672 | 10.2143 | 98.8397 |
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 |
| C12 | CD1 | LEU- 30 | 3.94 | 0 | Hydrophobic |
| F30 | CD1 | LEU- 30 | 3.42 | 0 | Hydrophobic |
| O2 | OD1 | ASP- 32 | 3.38 | 138.08 | H-Bond (Ligand Donor) |
| N2 | O | GLY- 34 | 2.65 | 139.34 | H-Bond (Ligand Donor) |
| CO | CB | SER- 35 | 3.47 | 0 | Hydrophobic |
| C17 | CD1 | TYR- 71 | 4.15 | 0 | Hydrophobic |
| C16 | CD1 | TYR- 71 | 4.04 | 0 | Hydrophobic |
| C27 | CB | TYR- 71 | 4.05 | 0 | Hydrophobic |
| F26 | CD2 | TYR- 71 | 4.11 | 0 | Hydrophobic |
| C3 | CB | THR- 72 | 3.85 | 0 | Hydrophobic |
| C13 | CG | GLN- 73 | 3.51 | 0 | Hydrophobic |
| C27 | CB | GLN- 73 | 4.34 | 0 | Hydrophobic |
| C4 | CB | GLN- 73 | 3.55 | 0 | Hydrophobic |
| F26 | CG | GLN- 73 | 3.24 | 0 | Hydrophobic |
| O1 | N | GLN- 73 | 3.19 | 171.04 | H-Bond (Protein Donor) |
| F26 | CD1 | PHE- 108 | 3.41 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 110 | 4.31 | 0 | Hydrophobic |
| F30 | CD1 | ILE- 110 | 3.77 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 110 | 4.08 | 0 | Hydrophobic |
| F30 | CH2 | TRP- 115 | 3.56 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 118 | 4 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 228 | 3.82 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 228 | 3.06 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 228 | 3.06 | 137.61 | H-Bond (Ligand Donor) |
| N1 | O | GLY- 230 | 3.07 | 165.15 | H-Bond (Ligand Donor) |
| C5 | CB | THR- 231 | 4.31 | 0 | Hydrophobic |
| C2 | CG2 | THR- 231 | 4.11 | 0 | Hydrophobic |
| O | N | THR- 232 | 3 | 141.2 | H-Bond (Protein Donor) |
| O | OG1 | THR- 232 | 2.9 | 143.69 | H-Bond (Protein Donor) |
