sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2012-06-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.400 | 7.400 | 7.400 | 0.000 | 7.400 | 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 |
|---|---|
| E | 100 % |
| B-Factor: | 20.999 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | IOD |
| Ligandability | Volume (Å3) |
|---|---|
| 0.810 | 864.000 |
| % Hydrophobic | % Polar |
|---|---|
| 36.72 | 63.28 |
| According to VolSite | |
| HET Code: | 0VA |
|---|---|
| Formula: | C20H20Cl2N5O2S |
| Molecular weight: | 465.376 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.4 % |
| Polar Surface area: | 143.1 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: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 32.8563 | 18.7532 | 75.0144 |
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 |
| CL2 | CD2 | LEU- 78 | 3.63 | 0 | Hydrophobic |
| C06 | CD2 | LEU- 78 | 3.94 | 0 | Hydrophobic |
| C20 | CE1 | TYR- 119 | 3.44 | 0 | Hydrophobic |
| CL1 | CD2 | TYR- 119 | 3.4 | 0 | Hydrophobic |
| C01 | CG2 | THR- 120 | 3.4 | 0 | Hydrophobic |
| C19 | CB | GLN- 121 | 3.89 | 0 | Hydrophobic |
| C11 | CB | GLN- 121 | 4.12 | 0 | Hydrophobic |
| CL1 | CG | GLN- 121 | 3.55 | 0 | Hydrophobic |
| O26 | NE2 | GLN- 121 | 3.44 | 151.24 | H-Bond (Protein Donor) |
| N23 | O | LYS- 155 | 3.5 | 155.13 | H-Bond (Ligand Donor) |
| CL1 | CD1 | PHE- 156 | 4.14 | 0 | Hydrophobic |
| CL2 | CD1 | ILE- 158 | 4.26 | 0 | Hydrophobic |
| CL2 | CZ2 | TRP- 163 | 3.55 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 166 | 4.12 | 0 | Hydrophobic |
| C06 | CD1 | ILE- 166 | 4.16 | 0 | Hydrophobic |
| C18 | CD1 | TYR- 246 | 3.68 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 274 | 3.29 | 0 | Hydrophobic |
| N22 | OD1 | ASP- 276 | 3.38 | 130.92 | H-Bond (Ligand Donor) |
| C02 | CG2 | THR- 279 | 4.1 | 0 | Hydrophobic |
| C11 | CD | ARG- 283 | 4.43 | 0 | Hydrophobic |
| C02 | CD | ARG- 283 | 3.97 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 283 | 3.89 | 24.93 | Pi/Cation |
| N21 | O | HOH- 667 | 3.01 | 179.97 | H-Bond (Protein Donor) |
