sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2014-09-23
| Name: | Glycosyltransferase |
|---|---|
| ID: | A4F1R4_CLITE |
| AC: | A4F1R4 |
| Organism: | Clitoria ternatea |
| Reign: | Eukaryota |
| TaxID: | 43366 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.044 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.701 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 47.17 | 52.83 |
| According to VolSite | |
| HET Code: | KMP |
|---|---|
| Formula: | C15H8O6 |
| Molecular weight: | 284.220 g/mol |
| DrugBank ID: | DB01852 |
| Buried Surface Area: | 64.75 % |
| Polar Surface area: | 112.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 52.605 | -3.8979 | 15.5923 |
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 |
| C16 | CB | PHE- 14 | 4.24 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 82 | 3.93 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 82 | 3.55 | 0 | Hydrophobic |
| C1 | CB | PRO- 179 | 4.39 | 0 | Hydrophobic |
| C6 | CB | ASP- 181 | 4.49 | 0 | Hydrophobic |
| O29 | OD2 | ASP- 181 | 2.67 | 167.27 | H-Bond (Ligand Donor) |
| C6 | CD2 | LEU- 196 | 3.51 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 274 | 4.09 | 0 | Hydrophobic |
| C19 | CE2 | PHE- 365 | 3.24 | 0 | Hydrophobic |
| C2 | CB | ASP- 367 | 4.04 | 0 | Hydrophobic |
