sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2002-04-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.000 | 7.000 | 7.000 | 0.000 | 7.000 | 1 |
| 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: | 21.701 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.327 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.57 | 49.43 |
| According to VolSite | |
| HET Code: | EH5 |
|---|---|
| Formula: | C46H51N3O10 |
| Molecular weight: | 805.911 g/mol |
| DrugBank ID: | DB03063 |
| Buried Surface Area: | 44.46 % |
| Polar Surface area: | 153.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 2 |
| Rings: | 7 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 16.0341 | 6.07971 | 27.633 |
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 |
| C37 | CG | MET- 15 | 4.2 | 0 | Hydrophobic |
| CE2 | CD1 | ILE- 32 | 3.45 | 0 | Hydrophobic |
| CB | CB | ASP- 34 | 4.43 | 0 | Hydrophobic |
| O1 | OD2 | ASP- 34 | 2.55 | 152.6 | H-Bond (Ligand Donor) |
| O1 | OD1 | ASP- 34 | 3.35 | 144.83 | H-Bond (Ligand Donor) |
| O2 | N | VAL- 78 | 3.09 | 130.83 | H-Bond (Protein Donor) |
| C8 | CG2 | VAL- 78 | 4.45 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 78 | 3.44 | 0 | Hydrophobic |
| O3 | OG | SER- 79 | 2.87 | 168.26 | H-Bond (Protein Donor) |
| C13 | CB | SER- 79 | 4.19 | 0 | Hydrophobic |
| CZ | CG2 | THR- 114 | 4.11 | 0 | Hydrophobic |
| CD1 | CD1 | ILE- 123 | 4 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 131 | 3.68 | 0 | Hydrophobic |
| C4 | CE2 | TYR- 192 | 3.87 | 0 | Hydrophobic |
| C6 | CE2 | TYR- 192 | 4.34 | 0 | Hydrophobic |
| O1 | OD2 | ASP- 214 | 2.58 | 163.03 | H-Bond (Protein Donor) |
| N2 | O | GLY- 216 | 2.97 | 153.42 | H-Bond (Ligand Donor) |
| C28 | CG2 | THR- 217 | 4.04 | 0 | Hydrophobic |
| O10 | OG | SER- 218 | 3.32 | 160.85 | H-Bond (Protein Donor) |
| C37 | CB | SER- 218 | 3.63 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 290 | 4.36 | 0 | Hydrophobic |
| C36 | CD1 | ILE- 290 | 4.04 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 292 | 4.11 | 0 | Hydrophobic |
| C8 | CE1 | PHE- 294 | 3.75 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 300 | 3.63 | 0 | Hydrophobic |
