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
2006-12-01
| Name: | Beta-glucosidase 1A |
|---|---|
| ID: | BGL1A_PHACH |
| AC: | Q25BW5 |
| Organism: | Phanerochaete chrysosporium |
| Reign: | Eukaryota |
| TaxID: | 5306 |
| EC Number: | 3.2.1.21 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 13.998 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.658 | 783.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.45 | 46.55 |
| According to VolSite | |
| HET Code: | LGC |
|---|---|
| Formula: | C6H10O6 |
| Molecular weight: | 178.140 g/mol |
| DrugBank ID: | DB04564 |
| Buried Surface Area: | 80.09 % |
| Polar Surface area: | 107.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -23.4445 | -16.7351 | 9.31192 |
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 |
| O3 | OE1 | GLN- 20 | 2.64 | 145.82 | H-Bond (Ligand Donor) |
| O4 | NE2 | GLN- 20 | 2.83 | 169.96 | H-Bond (Protein Donor) |
| O3 | NE2 | HIS- 123 | 3.02 | 154.46 | H-Bond (Protein Donor) |
| C2 | CH2 | TRP- 124 | 4.03 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 169 | 2.96 | 158.21 | H-Bond (Protein Donor) |
| C5 | CZ | TYR- 301 | 3.87 | 0 | Hydrophobic |
| O2 | OE1 | GLU- 365 | 2.62 | 144.79 | H-Bond (Ligand Donor) |
| C3 | CZ2 | TRP- 415 | 3.84 | 0 | Hydrophobic |
| C4 | CE2 | TRP- 415 | 3.82 | 0 | Hydrophobic |
| O4 | OE2 | GLU- 422 | 2.83 | 153.04 | H-Bond (Ligand Donor) |
| O6 | OE1 | GLU- 422 | 2.58 | 158.61 | H-Bond (Ligand Donor) |
| O3 | NE1 | TRP- 423 | 2.83 | 162.17 | H-Bond (Protein Donor) |
| C6 | CE2 | PHE- 431 | 3.45 | 0 | Hydrophobic |
