sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2014-12-06
| Name: | Oxygen-insensitive NAD(P)H nitroreductase |
|---|---|
| ID: | NFSB_ECOLI |
| AC: | P38489 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| G | 62 % |
| H | 38 % |
| B-Factor: | 53.056 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.941 | 1461.375 |
| % Hydrophobic | % Polar |
|---|---|
| 32.79 | 67.21 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 66.64 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -28.6598 | 44.598 | 3.23258 |
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 |
| C1' | CB | SER- 12 | 4.03 | 0 | Hydrophobic |
| C3' | CB | SER- 12 | 4.38 | 0 | Hydrophobic |
| O1P | N | SER- 12 | 3.02 | 154.56 | H-Bond (Protein Donor) |
| C8M | CB | PRO- 38 | 4.33 | 0 | Hydrophobic |
| C5' | CB | PRO- 38 | 4.48 | 0 | Hydrophobic |
| C7 | CB | SER- 40 | 3.75 | 0 | Hydrophobic |
| C4' | CB | ASN- 42 | 3.6 | 0 | Hydrophobic |
| C7M | CE2 | TYR- 144 | 4.03 | 0 | Hydrophobic |
| C7M | CD1 | LEU- 145 | 4.05 | 0 | Hydrophobic |
| C8M | CD1 | LEU- 145 | 3.66 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 162 | 4.4 | 0 | Hydrophobic |
| C1' | CG | PRO- 163 | 4.43 | 0 | Hydrophobic |
| C7 | CB | PRO- 163 | 4.16 | 0 | Hydrophobic |
| C8 | CG | PRO- 163 | 3.62 | 0 | Hydrophobic |
| C9 | CG | PRO- 163 | 3.35 | 0 | Hydrophobic |
| O4 | N | GLU- 165 | 3.34 | 135.49 | H-Bond (Protein Donor) |
| N5 | N | GLU- 165 | 3.11 | 151.56 | H-Bond (Protein Donor) |
| C6 | CG | GLU- 165 | 3.61 | 0 | Hydrophobic |
| O4 | N | GLY- 166 | 2.98 | 141.25 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 205 | 2.79 | 0 | Ionic (Protein Cationic) |
| O3P | NH2 | ARG- 207 | 2.57 | 156.63 | H-Bond (Protein Donor) |
| O3P | CZ | ARG- 207 | 3.5 | 0 | Ionic (Protein Cationic) |
