sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-09-12
| Name: | NAD(P)H dehydrogenase (quinone) |
|---|---|
| ID: | NQOR_ECOLI |
| AC: | P0A8G6 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 22 % |
| C | 78 % |
| B-Factor: | 18.916 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.949 | 749.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.24 | 56.76 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 69.03 % |
| 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 |
|---|---|---|
| -2.58935 | 1.57535 | 18.6457 |
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 |
| O2P | OG | SER- 9 | 2.65 | 147.71 | H-Bond (Protein Donor) |
| O3P | N | MET- 10 | 2.84 | 145.66 | H-Bond (Protein Donor) |
| O1P | N | TYR- 11 | 3.14 | 127.55 | H-Bond (Protein Donor) |
| O3P | N | TYR- 11 | 2.91 | 158.69 | H-Bond (Protein Donor) |
| C5' | CB | HIS- 13 | 4.27 | 0 | Hydrophobic |
| O1P | N | HIS- 13 | 2.7 | 163.32 | H-Bond (Protein Donor) |
| O2P | N | ILE- 14 | 2.82 | 167.1 | H-Bond (Protein Donor) |
| C4' | CB | PRO- 76 | 3.63 | 0 | Hydrophobic |
| O2' | O | THR- 77 | 2.63 | 167 | H-Bond (Ligand Donor) |
| C8 | CD | ARG- 78 | 3.24 | 0 | Hydrophobic |
| N5 | N | PHE- 79 | 2.94 | 165.51 | H-Bond (Protein Donor) |
| C7M | CE2 | PHE- 79 | 3.66 | 0 | Hydrophobic |
| C7M | CB | ASP- 91 | 4.39 | 0 | Hydrophobic |
| C4' | CB | SER- 112 | 4.35 | 0 | Hydrophobic |
| O4' | O | SER- 112 | 3.04 | 125.53 | H-Bond (Ligand Donor) |
| O4' | OG | SER- 112 | 2.6 | 162 | H-Bond (Protein Donor) |
| N1 | N | GLY- 114 | 2.96 | 143.19 | H-Bond (Protein Donor) |
| O2 | N | GLY- 114 | 2.73 | 139.98 | H-Bond (Protein Donor) |
| N3 | O | GLY- 117 | 2.71 | 155.62 | H-Bond (Ligand Donor) |
