sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
1988-02-04
| Name: | Reaction center protein L chain |
|---|---|
| ID: | RCEL_BLAVI |
| AC: | P06009 |
| Organism: | Blastochloris viridis |
| Reign: | Bacteria |
| TaxID: | 1079 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| L | 82 % |
| M | 14 % |
| H | 4 % |
| B-Factor: | 15.613 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | FE |
| Ligandability | Volume (Å3) |
|---|---|
| 1.320 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 70.00 | 30.00 |
| According to VolSite | |
| HET Code: | UQ1 |
|---|---|
| Formula: | C14H18O4 |
| Molecular weight: | 250.290 g/mol |
| DrugBank ID: | DB08689 |
| Buried Surface Area: | 68.35 % |
| Polar Surface area: | 52.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 131.85 | 71.5459 | -2.94878 |
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 |
| CM5 | CB | LEU- 189 | 3.83 | 0 | Hydrophobic |
| O4 | ND1 | HIS- 190 | 2.7 | 161.68 | H-Bond (Protein Donor) |
| CM3 | CD1 | ILE- 194 | 3.93 | 0 | Hydrophobic |
| CM2 | CB | GLU- 212 | 4.33 | 0 | Hydrophobic |
| CM5 | CZ | PHE- 216 | 3.36 | 0 | Hydrophobic |
| C7 | CD2 | PHE- 216 | 3.34 | 0 | Hydrophobic |
| C10 | CB | PHE- 216 | 4.26 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 220 | 4.28 | 0 | Hydrophobic |
| C7 | CB | SER- 223 | 4.49 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 224 | 4.16 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 224 | 4.49 | 0 | Hydrophobic |
| O1 | N | GLY- 225 | 2.7 | 156.12 | H-Bond (Protein Donor) |
| CM2 | CB | ALA- 226 | 4 | 0 | Hydrophobic |
| CM3 | CB | ALA- 226 | 3.89 | 0 | Hydrophobic |
| CM3 | CG2 | ILE- 229 | 4.04 | 0 | Hydrophobic |
| CM5 | CD1 | ILE- 229 | 4.17 | 0 | Hydrophobic |
