sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2013-03-24
| Name: | Ribosome inactivating protein |
|---|---|
| ID: | D9J2T9_MOMBA |
| AC: | D9J2T9 |
| Organism: | Momordica balsamina |
| Reign: | Eukaryota |
| TaxID: | 3672 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.536 |
|---|---|
| Number of residues: | 16 |
| Including | |
| Standard Amino Acids: | 16 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.163 | 398.250 |
| % Hydrophobic | % Polar |
|---|---|
| 47.46 | 52.54 |
| According to VolSite | |
| HET Code: | ASC |
|---|---|
| Formula: | C6H7O6 |
| Molecular weight: | 175.116 g/mol |
| DrugBank ID: | DB00126 |
| Buried Surface Area: | 56.48 % |
| Polar Surface area: | 110.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -15.5303 | -16.6807 | -7.60517 |
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 |
| C4 | CD1 | TYR- 70 | 3.89 | 0 | Hydrophobic |
| C5 | CG | TYR- 70 | 4.35 | 0 | Hydrophobic |
| O6 | N | ILE- 71 | 2.97 | 161.08 | H-Bond (Protein Donor) |
| O2 | N | TYR- 111 | 2.92 | 175.03 | H-Bond (Protein Donor) |
| C6 | CD1 | ILE- 155 | 3.79 | 0 | Hydrophobic |
