sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.050 Å
X-ray
2005-07-15
| Name: | Pentaerythritol tetranitrate reductase |
|---|---|
| ID: | P71278_ENTCL |
| AC: | P71278 |
| Organism: | Enterobacter cloacae |
| Reign: | Bacteria |
| TaxID: | 550 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 8.701 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.593 | 577.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.35 | 59.65 |
| According to VolSite | |
| HET Code: | STR |
|---|---|
| Formula: | C21H30O2 |
| Molecular weight: | 314.462 g/mol |
| DrugBank ID: | DB00396 |
| Buried Surface Area: | 63.22 % |
| Polar Surface area: | 34.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 6.2587 | 22.3841 | 18.3317 |
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 |
| C6 | CB | THR- 26 | 3.35 | 0 | Hydrophobic |
| C7 | CG2 | THR- 26 | 4 | 0 | Hydrophobic |
| C14 | CE2 | TYR- 68 | 3.63 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 68 | 3.74 | 0 | Hydrophobic |
| C21 | CB | ARG- 130 | 4.18 | 0 | Hydrophobic |
| C16 | CB | SER- 132 | 3.89 | 0 | Hydrophobic |
| O20 | NE | ARG- 142 | 2.83 | 160.14 | H-Bond (Protein Donor) |
| C21 | CD | ARG- 142 | 3.9 | 0 | Hydrophobic |
| O3 | NE2 | HIS- 181 | 3.05 | 158.67 | H-Bond (Protein Donor) |
| C2 | CB | HIS- 184 | 4.05 | 0 | Hydrophobic |
| O3 | ND1 | HIS- 184 | 2.87 | 158.66 | H-Bond (Protein Donor) |
| C2 | CE2 | TYR- 186 | 4.39 | 0 | Hydrophobic |
| C1 | CG | GLN- 241 | 4.48 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 275 | 4.18 | 0 | Hydrophobic |
| C15 | CE1 | TYR- 351 | 4.33 | 0 | Hydrophobic |
| C18 | CZ | TYR- 351 | 3.64 | 0 | Hydrophobic |
| C8 | CE1 | TYR- 351 | 4.01 | 0 | Hydrophobic |
| C6 | C6 | FMN- 1401 | 4.27 | 0 | Hydrophobic |
| C19 | C9A | FMN- 1401 | 3.56 | 0 | Hydrophobic |
