sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2005-03-31
| Name: | Reaction center protein L chain |
|---|---|
| ID: | RCEL_RHOSH |
| AC: | P0C0Y8 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 1063 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 86 % |
| B | 9 % |
| C | 5 % |
| B-Factor: | 25.064 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.301 | 347.625 |
| % Hydrophobic | % Polar |
|---|---|
| 76.70 | 23.30 |
| According to VolSite | |
| HET Code: | MST |
|---|---|
| Formula: | C10H19N5S |
| Molecular weight: | 241.356 g/mol |
| DrugBank ID: | DB08215 |
| Buried Surface Area: | 66.35 % |
| Polar Surface area: | 88.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 99.3257 | 27.0579 | 78.7905 |
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 |
| C8 | CB | LEU- 189 | 3.52 | 0 | Hydrophobic |
| S7 | CB | HIS- 190 | 4.04 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 193 | 3.78 | 0 | Hydrophobic |
| C16 | CB | GLU- 212 | 3.56 | 0 | Hydrophobic |
| S7 | CE1 | PHE- 216 | 3.99 | 0 | Hydrophobic |
| C8 | CZ | PHE- 216 | 4.1 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 216 | 3.46 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 216 | 3.78 | 0 | Aromatic Face/Face |
| C11 | CD2 | TYR- 222 | 3.73 | 0 | Hydrophobic |
| N14 | OG | SER- 223 | 2.94 | 133.03 | H-Bond (Ligand Donor) |
| C12 | CG2 | ILE- 224 | 4.24 | 0 | Hydrophobic |
| N5 | N | ILE- 224 | 3.12 | 149.45 | H-Bond (Protein Donor) |
| C16 | CG2 | THR- 226 | 4.16 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 229 | 3.45 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 232 | 3.92 | 0 | Hydrophobic |
