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
2009-08-03
| Name: | Peridinin-chlorophyll a-binding protein 1, chloroplastic |
|---|---|
| ID: | PCP1_AMPCA |
| AC: | P80484 |
| Organism: | Amphidinium carterae |
| Reign: | Eukaryota |
| TaxID: | 2961 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| M | 100 % |
| B-Factor: | 7.739 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.411 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 67.93 | 32.07 |
| According to VolSite | |
| HET Code: | PID |
|---|---|
| Formula: | C39H50O7 |
| Molecular weight: | 630.810 g/mol |
| DrugBank ID: | DB03001 |
| Buried Surface Area: | 31.69 % |
| Polar Surface area: | 105.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 12.5558 | 7.16889 | -11.1166 |
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 | MET- 47 | 3.97 | 0 | Hydrophobic |
| CM8 | CB | MET- 47 | 3.63 | 0 | Hydrophobic |
| CM8 | CG1 | ILE- 48 | 4.08 | 0 | Hydrophobic |
| CM5 | CG | MET- 50 | 3.92 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 59 | 4.08 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 59 | 3.53 | 0 | Hydrophobic |
| CM6 | CD2 | LEU- 59 | 3.98 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 104 | 3.9 | 0 | Hydrophobic |
| C13 | CB | TYR- 108 | 3.56 | 0 | Hydrophobic |
| CM1 | CE2 | TYR- 108 | 3.78 | 0 | Hydrophobic |
| CM4 | CD1 | TYR- 108 | 4.47 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 108 | 3.47 | 0 | Aromatic Face/Face |
| CM2 | CD2 | LEU- 140 | 3.77 | 0 | Hydrophobic |
