sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2013-09-25
| Name: | Phosphoethanolamine N-methyltransferase, putative |
|---|---|
| ID: | A5K867_PLAVS |
| AC: | A5K867 |
| Organism: | Plasmodium vivax |
| Reign: | Eukaryota |
| TaxID: | 126793 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 9.779 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.160 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 55.73 | 44.27 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 69.48 % |
| Polar Surface area: | 189.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 2.01352 | -16.7867 | -10.0812 |
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 |
| C3' | CZ | TYR- 16 | 3.74 | 0 | Hydrophobic |
| C2' | CE2 | TYR- 16 | 4.03 | 0 | Hydrophobic |
| SD | CZ | TYR- 16 | 4.02 | 0 | Hydrophobic |
| O | N | ILE- 33 | 2.91 | 167.43 | H-Bond (Protein Donor) |
| SD | CG1 | ILE- 33 | 3.86 | 0 | Hydrophobic |
| CB | CG1 | ILE- 33 | 3.69 | 0 | Hydrophobic |
| CG | CB | SER- 34 | 3.91 | 0 | Hydrophobic |
| CE | CB | SER- 34 | 4.28 | 0 | Hydrophobic |
| N | O | GLY- 60 | 2.77 | 148.16 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 82 | 2.74 | 173.65 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 82 | 3.46 | 127.67 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 82 | 2.57 | 150.41 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 83 | 3.27 | 147.86 | H-Bond (Protein Donor) |
| C1' | CG2 | ILE- 83 | 4.49 | 0 | Hydrophobic |
| C3' | SD | MET- 87 | 4.19 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 107 | 2.88 | 154.38 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 108 | 3.02 | 171.17 | H-Bond (Protein Donor) |
| N | O | ARG- 124 | 3.1 | 160.2 | H-Bond (Ligand Donor) |
| CE | CB | ASP- 125 | 4.47 | 0 | Hydrophobic |
| C5' | CB | SER- 126 | 3.85 | 0 | Hydrophobic |
| O | O | HOH- 593 | 2.75 | 153.9 | H-Bond (Protein Donor) |
