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
2006-04-06
| Name: | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial |
|---|---|
| ID: | ETFD_PIG |
| AC: | P55931 |
| Organism: | Sus scrofa |
| Reign: | Eukaryota |
| TaxID: | 9823 |
| EC Number: | 1.5.5.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 58.785 |
|---|---|
| Number of residues: | 75 |
| Including | |
| Standard Amino Acids: | 75 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.249 | 843.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.20 | 52.80 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 73.36 % |
| Polar Surface area: | 381.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 64.1118 | 32.0449 | 120.308 |
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' | CG | PRO- 45 | 3.97 | 0 | Hydrophobic |
| O1P | N | ALA- 46 | 2.53 | 161.23 | H-Bond (Protein Donor) |
| O3B | OE2 | GLU- 71 | 2.88 | 166.87 | H-Bond (Ligand Donor) |
| O2B | OE2 | GLU- 71 | 3.21 | 144.28 | H-Bond (Ligand Donor) |
| O2B | NZ | LYS- 72 | 2.61 | 127.5 | H-Bond (Protein Donor) |
| C1B | CB | LYS- 72 | 3.89 | 0 | Hydrophobic |
| C3B | CB | HIS- 79 | 4.37 | 0 | Hydrophobic |
| C8M | CD2 | LEU- 81 | 4.32 | 0 | Hydrophobic |
| C6 | CB | SER- 82 | 4.47 | 0 | Hydrophobic |
| C2' | CB | SER- 82 | 4.28 | 0 | Hydrophobic |
| C9A | CB | SER- 82 | 3.83 | 0 | Hydrophobic |
| O2' | OG | SER- 82 | 3.1 | 150 | H-Bond (Protein Donor) |
| N3 | O | CYS- 85 | 3.12 | 161.62 | H-Bond (Ligand Donor) |
| C2' | CD1 | LEU- 143 | 4.28 | 0 | Hydrophobic |
| N6A | O | ALA- 167 | 3.37 | 166.38 | H-Bond (Ligand Donor) |
| N1A | N | ALA- 167 | 3.18 | 166.71 | H-Bond (Protein Donor) |
| N6A | OE2 | GLU- 213 | 3.19 | 146.69 | H-Bond (Ligand Donor) |
| C7M | CE2 | PHE- 275 | 3.56 | 0 | Hydrophobic |
| O4 | OH | TYR- 277 | 3.32 | 142.74 | H-Bond (Protein Donor) |
| O2A | NH2 | ARG- 331 | 3.14 | 145.45 | H-Bond (Protein Donor) |
| C8M | CB | ARG- 331 | 4.3 | 0 | Hydrophobic |
| C8M | CD2 | LEU- 333 | 3.66 | 0 | Hydrophobic |
| C3' | SG | CYS- 354 | 4.13 | 0 | Hydrophobic |
| C5' | SG | CYS- 354 | 3.74 | 0 | Hydrophobic |
| O2P | N | CYS- 354 | 2.8 | 158.23 | H-Bond (Protein Donor) |
| C1' | CE | MET- 359 | 4.39 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 364 | 4.07 | 0 | Hydrophobic |
| N1 | N | GLY- 366 | 3.45 | 162.55 | H-Bond (Protein Donor) |
| N1 | OG1 | THR- 367 | 3.06 | 170.52 | H-Bond (Protein Donor) |
| C2' | CB | THR- 367 | 4.33 | 0 | Hydrophobic |
| C4' | CB | THR- 367 | 4.31 | 0 | Hydrophobic |
