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
2014-12-09
| Name: | Nitrogen regulatory PII-like protein |
|---|---|
| ID: | NRGB_BACSU |
| AC: | Q07428 |
| Organism: | Bacillus subtilis |
| Reign: | Bacteria |
| TaxID: | 224308 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 55 % |
| D | 45 % |
| B-Factor: | 47.033 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.239 | 533.250 |
| % Hydrophobic | % Polar |
|---|---|
| 39.24 | 60.76 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 58.89 % |
| 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 |
|---|---|---|
| -36.5352 | -18.2134 | 6.42352 |
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- 16 | 4.14 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 16 | 3.65 | 0 | Hydrophobic |
| O1G | OG1 | THR- 35 | 2.76 | 163.09 | H-Bond (Protein Donor) |
| O2G | OG | SER- 36 | 3.06 | 161.8 | H-Bond (Protein Donor) |
| O2' | OG1 | THR- 38 | 3.21 | 148.99 | H-Bond (Ligand Donor) |
| N3 | OG1 | THR- 38 | 2.78 | 143.81 | H-Bond (Protein Donor) |
| O3' | NH1 | ARG- 67 | 3.32 | 172.95 | H-Bond (Protein Donor) |
| C4' | CD | ARG- 67 | 3.34 | 0 | Hydrophobic |
| N6 | O | VAL- 73 | 2.9 | 158.07 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 73 | 2.92 | 154.55 | H-Bond (Protein Donor) |
| O2A | N | GLY- 96 | 2.77 | 134.98 | H-Bond (Protein Donor) |
| O2A | N | GLY- 98 | 3.32 | 148.92 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 99 | 2.7 | 123.1 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 99 | 3.3 | 154.54 | H-Bond (Protein Donor) |
| O3A | NZ | LYS- 99 | 3.32 | 142.94 | H-Bond (Protein Donor) |
| N7 | NZ | LYS- 99 | 3.07 | 150.57 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 99 | 2.7 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 99 | 3.52 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 99 | 3.3 | 0 | Ionic (Protein Cationic) |
