sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2001-06-04
| 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: | 10.599 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.836 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.37 | 56.63 |
| According to VolSite | |
| HET Code: | PDN |
|---|---|
| Formula: | C21H26O5 |
| Molecular weight: | 358.428 g/mol |
| DrugBank ID: | DB00635 |
| Buried Surface Area: | 56.76 % |
| Polar Surface area: | 94.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 21.5956 | 12.9588 | 17.8142 |
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 | 3.51 | 0 | Hydrophobic |
| C7 | CG2 | THR- 26 | 4.43 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 68 | 3.8 | 0 | Hydrophobic |
| O3 | O | ARG- 130 | 2.56 | 171.78 | H-Bond (Ligand Donor) |
| O1 | NE2 | HIS- 181 | 3.05 | 158.11 | H-Bond (Protein Donor) |
| C19 | CD1 | LEU- 275 | 4.05 | 0 | Hydrophobic |
| C15 | CZ | TYR- 351 | 4.12 | 0 | Hydrophobic |
| C18 | CE2 | TYR- 351 | 4.1 | 0 | Hydrophobic |
| C7 | CE1 | TYR- 351 | 3.79 | 0 | Hydrophobic |
| C8 | CZ | TYR- 351 | 3.86 | 0 | Hydrophobic |
| C6 | C6 | FMN- 1365 | 4.04 | 0 | Hydrophobic |
| C19 | C9A | FMN- 1365 | 3.62 | 0 | Hydrophobic |
