sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.380 Å
X-ray
2016-02-25
| Name: | Neutral alpha-glucosidase AB |
|---|---|
| ID: | GANAB_MOUSE |
| AC: | Q8BHN3 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 3.2.1.84 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.816 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.445 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 60.87 | 39.13 |
| According to VolSite | |
| HET Code: | NBV |
|---|---|
| Formula: | C10H22NO4 |
| Molecular weight: | 220.286 g/mol |
| DrugBank ID: | DB00419 |
| Buried Surface Area: | 72.56 % |
| Polar Surface area: | 85.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 5 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 107.72 | 531.731 | 70.5846 |
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 | CE3 | TRP- 423 | 3.66 | 0 | Hydrophobic |
| C15 | CH2 | TRP- 423 | 4 | 0 | Hydrophobic |
| O9 | OD1 | ASP- 451 | 2.7 | 160.76 | H-Bond (Ligand Donor) |
| O1 | OD2 | ASP- 451 | 2.56 | 173.22 | H-Bond (Ligand Donor) |
| C12 | CD1 | ILE- 452 | 4.02 | 0 | Hydrophobic |
| C10 | CH2 | TRP- 562 | 3.63 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 562 | 3.87 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 564 | 3.03 | 136.36 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 564 | 3.03 | 0 | Ionic (Ligand Cationic) |
| C14 | SD | MET- 565 | 3.49 | 0 | Hydrophobic |
| C16 | CZ | PHE- 571 | 3.52 | 0 | Hydrophobic |
| O7 | NH1 | ARG- 624 | 3.12 | 146.56 | H-Bond (Protein Donor) |
| C8 | CZ2 | TRP- 637 | 4 | 0 | Hydrophobic |
| O7 | OD1 | ASP- 640 | 2.62 | 162.66 | H-Bond (Ligand Donor) |
| C9 | CE1 | PHE- 673 | 3.66 | 0 | Hydrophobic |
| O1 | NE2 | HIS- 698 | 2.7 | 154.18 | H-Bond (Protein Donor) |
| O8 | O | HOH- 1142 | 2.73 | 174.65 | H-Bond (Ligand Donor) |
