sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2009-11-19
| Name: | NADH:flavin oxidoreductase/NADH oxidase |
|---|---|
| ID: | B0KAH1_THEP3 |
| AC: | B0KAH1 |
| Organism: | Thermoanaerobacter pseudethanolicus |
| Reign: | Bacteria |
| TaxID: | 340099 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 92 % |
| B | 8 % |
| B-Factor: | 10.048 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.634 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 36.53 | 63.47 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 65.64 % |
| 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 |
|---|---|---|
| 98.4618 | -4.90523 | 21.2583 |
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 |
| O2' | OG | SER- 22 | 2.64 | 157.95 | H-Bond (Protein Donor) |
| C3' | CB | SER- 22 | 4.29 | 0 | Hydrophobic |
| O2' | O | PRO- 23 | 2.62 | 153.49 | H-Bond (Ligand Donor) |
| C2' | CG | MET- 24 | 4 | 0 | Hydrophobic |
| C6 | CB | MET- 24 | 3.48 | 0 | Hydrophobic |
| C9 | CG | MET- 24 | 3.83 | 0 | Hydrophobic |
| N5 | N | CYS- 25 | 2.72 | 160.45 | H-Bond (Protein Donor) |
| C6 | CB | CYS- 25 | 4.06 | 0 | Hydrophobic |
| C7M | CE | MET- 26 | 4.42 | 0 | Hydrophobic |
| O4 | N | ALA- 58 | 3.09 | 166.13 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 100 | 2.82 | 178.76 | H-Bond (Protein Donor) |
| N3 | OE1 | GLN- 100 | 2.83 | 167.46 | H-Bond (Ligand Donor) |
| O2 | NH1 | ARG- 216 | 2.78 | 127.48 | H-Bond (Protein Donor) |
| O2' | NH1 | ARG- 216 | 3.31 | 139.5 | H-Bond (Protein Donor) |
| O3' | NH1 | ARG- 216 | 3.06 | 143.79 | H-Bond (Protein Donor) |
| C3' | CG2 | VAL- 283 | 4.01 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 283 | 4.02 | 0 | Hydrophobic |
| O2P | N | LEU- 285 | 2.74 | 157.04 | H-Bond (Protein Donor) |
| O3P | N | GLY- 307 | 2.82 | 144.05 | H-Bond (Protein Donor) |
| C8M | CG | ARG- 308 | 3.78 | 0 | Hydrophobic |
| O1P | N | ARG- 308 | 2.82 | 163.56 | H-Bond (Protein Donor) |
| O1P | NE | ARG- 308 | 2.91 | 160.06 | H-Bond (Protein Donor) |
| O2P | NH2 | ARG- 308 | 2.77 | 158.58 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 308 | 3.73 | 0 | Ionic (Protein Cationic) |
| O2P | CZ | ARG- 308 | 3.56 | 0 | Ionic (Protein Cationic) |
| C8M | CB | ARG- 333 | 4.15 | 0 | Hydrophobic |
| O3P | O | HOH- 349 | 2.71 | 179.97 | H-Bond (Protein Donor) |
| O3P | O | HOH- 367 | 2.75 | 179.94 | H-Bond (Protein Donor) |
| O3' | O | HOH- 447 | 2.66 | 179.95 | H-Bond (Protein Donor) |
