sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2007-09-13
| Name: | Beta-galactoside-specific lectin 1 |
|---|---|
| ID: | ML1_VISAL |
| AC: | P81446 |
| Organism: | Viscum album |
| Reign: | Eukaryota |
| TaxID: | 3972 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 52 % |
| B | 48 % |
| B-Factor: | 43.554 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.939 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.89 | 49.11 |
| According to VolSite | |
| HET Code: | SGI |
|---|---|
| Formula: | C9H11NO2 |
| Molecular weight: | 165.189 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.72 % |
| Polar Surface area: | 63.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 49.044 | 48.0882 | -1.04867 |
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 |
| CE1 | CG1 | VAL- 228 | 3.61 | 0 | Hydrophobic |
| CZ | CG2 | VAL- 228 | 3.54 | 0 | Hydrophobic |
| CD1 | CD1 | LEU- 230 | 4.05 | 0 | Hydrophobic |
| CD1 | CB | ASP- 235 | 4.15 | 0 | Hydrophobic |
| CA | CB | ARG- 388 | 3.7 | 0 | Hydrophobic |
| CE2 | CB | ARG- 388 | 3.74 | 0 | Hydrophobic |
| CE1 | CD | ARG- 388 | 3.43 | 0 | Hydrophobic |
| CD2 | CG2 | THR- 390 | 3.85 | 0 | Hydrophobic |
| CA | CG2 | THR- 390 | 4.09 | 0 | Hydrophobic |
| CA | CD1 | LEU- 423 | 4.02 | 0 | Hydrophobic |
| CD2 | CB | PRO- 510 | 3.81 | 0 | Hydrophobic |
| OH | O | HOH- 677 | 3.03 | 140.14 | H-Bond (Ligand Donor) |
