sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 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: | 9.406 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.351 | 567.000 |
| % Hydrophobic | % Polar |
|---|---|
| 69.05 | 30.95 |
| According to VolSite | |
| HET Code: | PID |
|---|---|
| Formula: | C39H50O7 |
| Molecular weight: | 630.810 g/mol |
| DrugBank ID: | DB03001 |
| Buried Surface Area: | 36.99 % |
| 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 |
|---|---|---|
| 1.39611 | -11.8008 | 3.54485 |
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 |
| CM4 | CZ | PHE- 17 | 3.88 | 0 | Hydrophobic |
| CM4 | CG2 | VAL- 21 | 3.72 | 0 | Hydrophobic |
| CM5 | CB | PHE- 28 | 3.73 | 0 | Hydrophobic |
| CM8 | CB | PHE- 28 | 3.86 | 0 | Hydrophobic |
| C28 | CB | LEU- 29 | 4.16 | 0 | Hydrophobic |
| C31 | CD2 | LEU- 29 | 4.21 | 0 | Hydrophobic |
| CM8 | CB | LEU- 29 | 3.97 | 0 | Hydrophobic |
| CM1 | CB | PRO- 120 | 3.7 | 0 | Hydrophobic |
| CM1 | CB | ALA- 121 | 4.4 | 0 | Hydrophobic |
| C13 | CB | MET- 123 | 3.65 | 0 | Hydrophobic |
| CM4 | SD | MET- 123 | 3.94 | 0 | Hydrophobic |
| CM2 | CD | LYS- 124 | 4.42 | 0 | Hydrophobic |
| C1 | CD | LYS- 124 | 3.85 | 0 | Hydrophobic |
| O2 | NZ | LYS- 124 | 2.81 | 163.25 | H-Bond (Protein Donor) |
| CM2 | CB | ALA- 132 | 4.16 | 0 | Hydrophobic |
| CM2 | CG | GLU- 133 | 4.46 | 0 | Hydrophobic |
| CM2 | CB | TYR- 136 | 4.05 | 0 | Hydrophobic |
| CM3 | CG | TYR- 136 | 3.52 | 0 | Hydrophobic |
