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
2013-03-05
| Name: | Nodulin-13 |
|---|---|
| ID: | NOD13_MEDTR |
| AC: | P93330 |
| Organism: | Medicago truncatula |
| Reign: | Eukaryota |
| TaxID: | 3880 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.973 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.964 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.65 | 41.35 |
| According to VolSite | |
| HET Code: | EMU |
|---|---|
| Formula: | C12H11N5 |
| Molecular weight: | 225.249 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.82 % |
| Polar Surface area: | 66.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 37.5105 | 14.9244 | 11.9121 |
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 |
| N9 | NE2 | GLN- 68 | 3.12 | 170.33 | H-Bond (Protein Donor) |
| N3 | OH | TYR- 82 | 2.79 | 167.41 | H-Bond (Protein Donor) |
| C14 | CD1 | ILE- 98 | 3.81 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 100 | 3.98 | 0 | Aromatic Face/Face |
| C12 | CB | ALA- 136 | 3.93 | 0 | Hydrophobic |
| C9 | CG | ARG- 140 | 3.58 | 0 | Hydrophobic |
| C11 | CB | ARG- 140 | 4.23 | 0 | Hydrophobic |
