sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2004-10-18
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.600 | 7.600 | 7.600 | 0.000 | 7.600 | 3 |
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 42.772 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.976 | 840.375 |
| % Hydrophobic | % Polar |
|---|---|
| 38.55 | 61.45 |
| According to VolSite | |
| HET Code: | MMI |
|---|---|
| Formula: | C38H62N6O8 |
| Molecular weight: | 730.934 g/mol |
| DrugBank ID: | DB02378 |
| Buried Surface Area: | 43.99 % |
| Polar Surface area: | 204.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 7 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| 46.7099 | 19.7434 | 108.4 |
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 |
| C36 | CD1 | LEU- 30 | 4.25 | 0 | Hydrophobic |
| C44 | CB | SER- 35 | 3.55 | 0 | Hydrophobic |
| C35 | CB | TYR- 71 | 4.43 | 0 | Hydrophobic |
| C38 | CD1 | TYR- 71 | 3.96 | 0 | Hydrophobic |
| C37 | CD1 | TYR- 71 | 3.67 | 0 | Hydrophobic |
| C44 | CE1 | TYR- 71 | 3.32 | 0 | Hydrophobic |
| C22 | CG2 | THR- 72 | 3.91 | 0 | Hydrophobic |
| C39 | CB | THR- 72 | 4.09 | 0 | Hydrophobic |
| O32 | OG1 | THR- 72 | 3.19 | 177.11 | H-Bond (Protein Donor) |
| O32 | N | THR- 72 | 2.98 | 161.17 | H-Bond (Protein Donor) |
| O12 | OE1 | GLN- 73 | 2.62 | 162.81 | H-Bond (Ligand Donor) |
| O21 | N | GLN- 73 | 3.1 | 130.29 | H-Bond (Protein Donor) |
| C35 | CD1 | PHE- 108 | 3.84 | 0 | Hydrophobic |
| C36 | CE1 | PHE- 108 | 4.16 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 110 | 3.91 | 0 | Hydrophobic |
| C36 | CH2 | TRP- 115 | 3.66 | 0 | Hydrophobic |
| C43 | CB | ILE- 126 | 4.5 | 0 | Hydrophobic |
| N3 | O | GLY- 230 | 3.43 | 154.18 | H-Bond (Ligand Donor) |
| C22 | CG2 | THR- 231 | 4.06 | 0 | Hydrophobic |
| C25 | CB | THR- 232 | 3.46 | 0 | Hydrophobic |
| C25 | CB | ASN- 233 | 3.72 | 0 | Hydrophobic |
