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
2012-06-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.700 | 7.700 | 7.700 | 0.000 | 7.700 | 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: | 24.634 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | IOD |
| Ligandability | Volume (Å3) |
|---|---|
| 0.518 | 732.375 |
| % Hydrophobic | % Polar |
|---|---|
| 30.41 | 69.59 |
| According to VolSite | |
| HET Code: | 0VB |
|---|---|
| Formula: | C23H25ClN5O3S |
| Molecular weight: | 486.994 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.19 % |
| Polar Surface area: | 146.18 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: | 8 |
| X | Y | Z |
|---|---|---|
| -4.01312 | 14.4141 | 32.1381 |
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 |
| C19 | CD2 | LEU- 78 | 3.68 | 0 | Hydrophobic |
| CL1 | CD2 | TYR- 119 | 3.91 | 0 | Hydrophobic |
| C03 | CB | THR- 120 | 4.45 | 0 | Hydrophobic |
| C04 | CG | GLN- 121 | 4.27 | 0 | Hydrophobic |
| C12 | CB | GLN- 121 | 4.11 | 0 | Hydrophobic |
| C22 | CB | GLN- 121 | 4.12 | 0 | Hydrophobic |
| CL1 | CG | GLN- 121 | 3.62 | 0 | Hydrophobic |
| O29 | NE2 | GLN- 121 | 3.43 | 165.22 | H-Bond (Protein Donor) |
| N27 | O | PHE- 156 | 2.62 | 172.06 | H-Bond (Ligand Donor) |
| CL1 | CD1 | PHE- 156 | 3.81 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 158 | 3.81 | 0 | Hydrophobic |
| C21 | CG1 | ILE- 158 | 3.61 | 0 | Hydrophobic |
| C19 | CZ2 | TRP- 163 | 3.74 | 0 | Hydrophobic |
| C05 | CD1 | ILE- 166 | 4.3 | 0 | Hydrophobic |
| C20 | CE1 | TYR- 246 | 3.29 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 274 | 3.35 | 0 | Hydrophobic |
| N25 | OD2 | ASP- 276 | 2.57 | 150.06 | H-Bond (Ligand Donor) |
| N25 | OD1 | ASP- 276 | 3.38 | 126.01 | H-Bond (Ligand Donor) |
| N26 | OD1 | ASP- 276 | 2.91 | 140.02 | H-Bond (Ligand Donor) |
| C02 | CG2 | THR- 279 | 3.56 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 283 | 3.82 | 26.91 | Pi/Cation |
| C02 | CD | ARG- 283 | 3.93 | 0 | Hydrophobic |
