sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2016-03-05
| 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: | 23.565 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.083 | 394.875 |
| % Hydrophobic | % Polar |
|---|---|
| 37.61 | 62.39 |
| According to VolSite | |
| HET Code: | URI |
|---|---|
| Formula: | C9H12N2O6 |
| Molecular weight: | 244.201 g/mol |
| DrugBank ID: | DB02745 |
| Buried Surface Area: | 68.33 % |
| Polar Surface area: | 119.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -15.6779 | -16.4941 | -9.56188 |
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 |
| C3' | CE1 | TYR- 70 | 3.47 | 0 | Hydrophobic |
| N3 | O | ILE- 71 | 2.84 | 164.12 | H-Bond (Ligand Donor) |
| O2 | N | ILE- 71 | 2.99 | 154.71 | H-Bond (Protein Donor) |
| O4 | OE2 | GLU- 85 | 2.5 | 161.78 | H-Bond (Protein Donor) |
| C5' | CB | ASN- 110 | 4.01 | 0 | Hydrophobic |
| O5' | N | TYR- 111 | 2.95 | 172.96 | H-Bond (Protein Donor) |
| C4' | CD2 | TYR- 111 | 3.95 | 0 | Hydrophobic |
| O5' | OE1 | GLU- 112 | 3.45 | 131.95 | H-Bond (Ligand Donor) |
| C1' | CG2 | ILE- 155 | 4.23 | 0 | Hydrophobic |
| O2' | NH2 | ARG- 163 | 3.41 | 133.24 | H-Bond (Protein Donor) |
| O2' | NH1 | ARG- 163 | 2.89 | 160 | H-Bond (Protein Donor) |
| O3' | NH1 | ARG- 163 | 3.37 | 126.6 | H-Bond (Protein Donor) |
| O3' | O | HOH- 924 | 2.71 | 150.25 | H-Bond (Ligand Donor) |
