sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.560 Å
X-ray
2005-02-08
| Name: | Plasmepsin-2 |
|---|---|
| ID: | PLM2_PLAFA |
| AC: | P46925 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 5833 |
| EC Number: | 3.4.23.39 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.168 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.395 | 725.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.09 | 47.91 |
| According to VolSite | |
| HET Code: | IH4 |
|---|---|
| Formula: | C37H45N4O3 |
| Molecular weight: | 593.778 g/mol |
| DrugBank ID: | DB02505 |
| Buried Surface Area: | 33.75 % |
| Polar Surface area: | 79.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| -0.729614 | 67.5854 | 10.2061 |
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 |
| C43 | CG2 | ILE- 14 | 3.59 | 0 | Hydrophobic |
| C5 | CG2 | THR- 114 | 4.17 | 0 | Hydrophobic |
| N10 | OG1 | THR- 114 | 2.72 | 150.96 | H-Bond (Protein Donor) |
| O1 | N | SER- 218 | 2.87 | 163.9 | H-Bond (Protein Donor) |
| C36 | CB | SER- 218 | 3.93 | 0 | Hydrophobic |
| C42 | CB | ALA- 219 | 4.49 | 0 | Hydrophobic |
| C36 | CB | ALA- 219 | 4.01 | 0 | Hydrophobic |
| C42 | CD2 | PHE- 244 | 4.14 | 0 | Hydrophobic |
| C41 | CE2 | PHE- 244 | 3.7 | 0 | Hydrophobic |
| C40 | SD | MET- 286 | 3.89 | 0 | Hydrophobic |
| C35 | CD1 | ILE- 290 | 4 | 0 | Hydrophobic |
| C42 | CG1 | ILE- 290 | 3.71 | 0 | Hydrophobic |
| C30 | CD1 | LEU- 292 | 3.76 | 0 | Hydrophobic |
| C31 | CD2 | LEU- 292 | 4.02 | 0 | Hydrophobic |
| C29 | CE1 | PHE- 294 | 4.4 | 0 | Hydrophobic |
