sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.960 Å
X-ray
2006-08-25
| 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 |
|---|---|
| H | 4 % |
| L | 84 % |
| M | 12 % |
| B-Factor: | 21.660 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.397 | 324.000 |
| % Hydrophobic | % Polar |
|---|---|
| 71.88 | 28.13 |
| According to VolSite | |
| HET Code: | UQ1 |
|---|---|
| Formula: | C14H18O4 |
| Molecular weight: | 250.290 g/mol |
| DrugBank ID: | DB08689 |
| Buried Surface Area: | 72.36 % |
| 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 |
|---|---|---|
| 130.198 | 69.7608 | -3.00722 |
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 | 3.75 | 0 | Hydrophobic |
| O4 | ND1 | HIS- 190 | 2.58 | 163.72 | H-Bond (Protein Donor) |
| CM5 | CB | HIS- 190 | 4.32 | 0 | Hydrophobic |
| CM2 | CD2 | LEU- 193 | 4.48 | 0 | Hydrophobic |
| CM3 | CD2 | LEU- 193 | 3.53 | 0 | Hydrophobic |
| CM3 | CD1 | ILE- 194 | 3.57 | 0 | Hydrophobic |
| CM2 | CB | GLU- 212 | 3.82 | 0 | Hydrophobic |
| CM3 | CG | GLU- 212 | 4.49 | 0 | Hydrophobic |
| CM5 | CE2 | PHE- 216 | 3.62 | 0 | Hydrophobic |
| C7 | CD2 | PHE- 216 | 3.34 | 0 | Hydrophobic |
| C10 | CB | PHE- 216 | 4.5 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 220 | 4.22 | 0 | Hydrophobic |
| C10 | CD2 | TYR- 222 | 4.03 | 0 | Hydrophobic |
| O1 | OG | SER- 223 | 2.61 | 171.83 | H-Bond (Protein Donor) |
| O1 | N | ILE- 224 | 2.74 | 128.59 | H-Bond (Protein Donor) |
| C11 | CB | ILE- 224 | 4.03 | 0 | Hydrophobic |
| O2 | N | GLY- 225 | 3 | 125.17 | H-Bond (Protein Donor) |
| CM5 | CD1 | ILE- 229 | 4.06 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 232 | 4.12 | 0 | Hydrophobic |
