sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2015-10-11
| Name: | 1,4-alpha-glucan branching enzyme GlgB |
|---|---|
| ID: | GLGB_ECO24 |
| AC: | A7ZSW5 |
| Organism: | Escherichia coli O139:H28 |
| Reign: | Bacteria |
| TaxID: | 331111 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 76 % |
| D | 24 % |
| B-Factor: | 63.509 |
|---|---|
| Number of residues: | 18 |
| Including | |
| Standard Amino Acids: | 17 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.411 | 924.750 |
| % Hydrophobic | % Polar |
|---|---|
| 36.86 | 63.14 |
| According to VolSite | |
| HET Code: | ACX |
|---|---|
| Formula: | C36H60O30 |
| Molecular weight: | 972.844 g/mol |
| DrugBank ID: | DB01909 |
| Buried Surface Area: | 19.59 % |
| Polar Surface area: | 474.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 30 |
| H-Bond Donors: | 18 |
| Rings: | 8 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 24.0333 | 60.2586 | 41.0371 |
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 |
| O2E | O | ASN- 259 | 2.85 | 154.76 | H-Bond (Ligand Donor) |
| C3F | CB | ASN- 259 | 4.16 | 0 | Hydrophobic |
| C3A | CZ | PHE- 261 | 4.44 | 0 | Hydrophobic |
| C5A | CZ | PHE- 261 | 4.5 | 0 | Hydrophobic |
| C4C | CE2 | PHE- 261 | 4.4 | 0 | Hydrophobic |
| C3D | CD1 | PHE- 261 | 3.96 | 0 | Hydrophobic |
| C3F | CE1 | PHE- 261 | 4.46 | 0 | Hydrophobic |
| C3C | CD2 | PHE- 261 | 4 | 0 | Hydrophobic |
| C3B | CE2 | PHE- 261 | 3.93 | 0 | Hydrophobic |
| C1C | CE3 | TRP- 262 | 4.07 | 0 | Hydrophobic |
| C2D | CD2 | TRP- 262 | 4.09 | 0 | Hydrophobic |
| C3D | CE3 | TRP- 262 | 3.89 | 0 | Hydrophobic |
| C6D | CZ3 | TRP- 262 | 3.46 | 0 | Hydrophobic |
| O3D | N | TRP- 262 | 2.81 | 162.64 | H-Bond (Protein Donor) |
