sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2011-06-20
| Name: | Nodulation protein Z |
|---|---|
| ID: | Q9AQ17_BRASW |
| AC: | Q9AQ17 |
| Organism: | Bradyrhizobium sp. |
| Reign: | Bacteria |
| TaxID: | 133505 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 51.924 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.545 | 695.250 |
| % Hydrophobic | % Polar |
|---|---|
| 38.35 | 61.65 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 36 % |
| Polar Surface area: | 276.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 18.268 | 44.279 | 7.18679 |
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 |
| N7 | NE2 | HIS- 175 | 2.79 | 171.68 | H-Bond (Protein Donor) |
| C5' | CD | ARG- 177 | 4.04 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 177 | 3.63 | 13.37 | Pi/Cation |
| N1 | OD2 | ASP- 270 | 2.97 | 151.3 | H-Bond (Ligand Donor) |
| C2' | CD2 | PHE- 289 | 4.36 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 289 | 3.81 | 0 | Aromatic Face/Face |
