sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-02-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.960 | 6.960 | 6.960 | 0.000 | 6.960 | 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: | 20.091 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.019 | 918.000 |
| % Hydrophobic | % Polar |
|---|---|
| 33.82 | 66.18 |
| According to VolSite | |
| HET Code: | 0KP |
|---|---|
| Formula: | C21H19N4O |
| Molecular weight: | 343.402 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.36 % |
| Polar Surface area: | 70.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 23.7557 | 10.8046 | 21.2534 |
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 |
| C15 | CD2 | LEU- 91 | 3.85 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 93 | 2.67 | 159.21 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 93 | 3.42 | 121.52 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 93 | 2.77 | 164 | H-Bond (Ligand Donor) |
| C3 | OD2 | ASP- 93 | 3.5 | 0 | Ionic (Ligand Cationic) |
| C3 | OD1 | ASP- 93 | 3.47 | 0 | Ionic (Ligand Cationic) |
| C7 | CB | SER- 96 | 3.6 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 130 | 3.82 | 0 | Hydrophobic |
| C9 | CD1 | TYR- 132 | 3.36 | 0 | Hydrophobic |
| C9 | CB | TYR- 132 | 3.98 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 171 | 3.59 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 179 | 3.57 | 0 | Hydrophobic |
| C3 | OD2 | ASP- 289 | 3.79 | 0 | Ionic (Ligand Cationic) |
| N3 | OD2 | ASP- 289 | 2.72 | 156.14 | H-Bond (Ligand Donor) |
