sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2011-08-03
| Name: | Nitrogen regulatory protein P-II (GlnB-3) |
|---|---|
| ID: | O28524_ARCFU |
| AC: | O28524 |
| Organism: | Archaeoglobus fulgidus |
| Reign: | Archaea |
| TaxID: | 224325 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 55 % |
| B | 42 % |
| E | 3 % |
| B-Factor: | 60.170 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.453 | 1015.875 |
| % Hydrophobic | % Polar |
|---|---|
| 38.54 | 61.46 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 72.49 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -55.5404 | -11.5769 | -17.0296 |
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' | CG1 | VAL- 7 | 4 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 7 | 4.03 | 0 | Hydrophobic |
| C2' | CB | THR- 29 | 4.45 | 0 | Hydrophobic |
| O2' | OG1 | THR- 29 | 2.93 | 150.9 | H-Bond (Ligand Donor) |
| N3 | OG1 | THR- 29 | 2.67 | 141.09 | H-Bond (Protein Donor) |
| C4' | CD | LYS- 58 | 4.39 | 0 | Hydrophobic |
| N6 | O | VAL- 64 | 3.1 | 154.96 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 64 | 2.92 | 173.22 | H-Bond (Protein Donor) |
| O1G | N | GLY- 87 | 3.45 | 173.68 | H-Bond (Protein Donor) |
| O1A | N | GLY- 89 | 3.1 | 149.73 | H-Bond (Protein Donor) |
| O2G | CZ | ARG- 90 | 3.87 | 0 | Ionic (Protein Cationic) |
| O2A | CZ | ARG- 90 | 3.24 | 0 | Ionic (Protein Cationic) |
| O2G | NH2 | ARG- 90 | 3.13 | 157.03 | H-Bond (Protein Donor) |
| O1G | NH1 | ARG- 103 | 3.36 | 143.06 | H-Bond (Protein Donor) |
| O3G | CZ | ARG- 103 | 3.54 | 0 | Ionic (Protein Cationic) |
