sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.240 Å
X-ray
2004-08-18
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.660 | 8.870 | 8.660 | 0.300 | 9.300 | 3 |
| 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: | 29.540 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.413 | 1005.750 |
| % Hydrophobic | % Polar |
|---|---|
| 46.98 | 53.02 |
| According to VolSite | |
| HET Code: | TIT |
|---|---|
| Formula: | C32H45BrN6O7 |
| Molecular weight: | 705.640 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.74 % |
| Polar Surface area: | 201.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 6 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 11.9581 | 8.4103 | 23.5766 |
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 |
| C27 | CD1 | ILE- 32 | 3.61 | 0 | Hydrophobic |
| O04 | OD2 | ASP- 34 | 2.76 | 151.52 | H-Bond (Ligand Donor) |
| O04 | OD1 | ASP- 34 | 3.09 | 139.95 | H-Bond (Ligand Donor) |
| N03 | O | GLY- 36 | 3.17 | 174.39 | H-Bond (Ligand Donor) |
| C28 | CB | SER- 37 | 4.46 | 0 | Hydrophobic |
| C28 | CE | MET- 75 | 4.22 | 0 | Hydrophobic |
| N02 | O | ASN- 76 | 3.16 | 164.02 | H-Bond (Ligand Donor) |
| C23 | CB | TYR- 77 | 4.49 | 0 | Hydrophobic |
| C20 | CD2 | TYR- 77 | 3.89 | 0 | Hydrophobic |
| C07 | CD2 | TYR- 77 | 4.15 | 0 | Hydrophobic |
| C28 | CD2 | TYR- 77 | 4.46 | 0 | Hydrophobic |
| O03 | N | VAL- 78 | 2.64 | 146.37 | H-Bond (Protein Donor) |
| C31 | CG2 | VAL- 78 | 4.04 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 78 | 4.37 | 0 | Hydrophobic |
| C17 | CB | VAL- 78 | 3.74 | 0 | Hydrophobic |
| N05 | OG | SER- 79 | 3.3 | 148.35 | H-Bond (Ligand Donor) |
| O05 | N | SER- 79 | 3.39 | 152.55 | H-Bond (Protein Donor) |
| N06 | OG | SER- 79 | 2.65 | 141.54 | H-Bond (Protein Donor) |
| C24 | CB | SER- 79 | 4.22 | 0 | Hydrophobic |
| BR | CD2 | PHE- 111 | 3.63 | 0 | Hydrophobic |
| BR | CB | THR- 114 | 3.34 | 0 | Hydrophobic |
| C15 | CG2 | THR- 114 | 3.81 | 0 | Hydrophobic |
| C26 | CG2 | THR- 114 | 3.89 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 123 | 4.34 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 131 | 4.46 | 0 | Hydrophobic |
| N04 | OG1 | THR- 217 | 3.28 | 148.8 | H-Bond (Ligand Donor) |
| C18 | CG2 | THR- 217 | 4.33 | 0 | Hydrophobic |
| C19 | CG2 | THR- 217 | 4.22 | 0 | Hydrophobic |
| C13 | CB | SER- 218 | 4.34 | 0 | Hydrophobic |
| O06 | N | SER- 218 | 3.22 | 153.22 | H-Bond (Protein Donor) |
| C19 | CG2 | THR- 221 | 4.26 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 300 | 3.75 | 0 | Hydrophobic |
