sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
2014-08-15
| Name: | Flavodoxin 2 |
|---|---|
| ID: | FLAW_ECOLI |
| AC: | P0ABY4 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.813 | 415.125 |
| % Hydrophobic | % Polar |
|---|---|
| 50.41 | 49.59 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 67.66 % |
| 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 |
|---|---|---|
| -2.46042 | 15.1046 | -30.2855 |
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 | N | SER- 10 | 3.16 | 171.63 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 11 | 2.67 | 159.99 | H-Bond (Protein Donor) |
| C5' | CD2 | TYR- 13 | 3.79 | 0 | Hydrophobic |
| O3P | N | THR- 14 | 3.28 | 161.8 | H-Bond (Protein Donor) |
| C5' | CB | PRO- 54 | 3.58 | 0 | Hydrophobic |
| O2' | O | THR- 55 | 2.66 | 145.45 | H-Bond (Ligand Donor) |
| C7M | CZ3 | TRP- 56 | 4.14 | 0 | Hydrophobic |
| C8M | CZ3 | TRP- 56 | 3.67 | 0 | Hydrophobic |
| C5' | CE2 | TRP- 56 | 4.09 | 0 | Hydrophobic |
| O2P | NE1 | TRP- 56 | 2.88 | 161.13 | H-Bond (Protein Donor) |
| O4 | N | GLY- 59 | 3.01 | 154.24 | H-Bond (Protein Donor) |
| C4' | CB | LEU- 87 | 3.67 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 87 | 4.48 | 0 | Hydrophobic |
| O2 | N | ASP- 89 | 2.9 | 163.15 | H-Bond (Protein Donor) |
| N3 | O | TRP- 96 | 3.01 | 152.19 | H-Bond (Ligand Donor) |
