sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2013-05-16
| Name: | Phosphoethanolamine N-methyltransferase 2 |
|---|---|
| ID: | U5HK48_HAECO |
| AC: | U5HK48 |
| Organism: | Haemonchus contortus |
| Reign: | Eukaryota |
| TaxID: | 6289 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 69.009 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.811 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.98 | 53.02 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 79.37 % |
| 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 |
|---|---|---|
| -41.1385 | 74.0499 | 85.9292 |
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 |
| C2' | CD1 | LEU- 178 | 4.48 | 0 | Hydrophobic |
| C3' | CE2 | TYR- 183 | 3.4 | 0 | Hydrophobic |
| SD | CZ | TYR- 183 | 3.98 | 0 | Hydrophobic |
| O | N | ILE- 200 | 3.27 | 162.71 | H-Bond (Protein Donor) |
| OXT | N | ILE- 200 | 2.83 | 132.12 | H-Bond (Protein Donor) |
| SD | CB | ILE- 200 | 4.45 | 0 | Hydrophobic |
| CE | CG2 | ILE- 200 | 4.21 | 0 | Hydrophobic |
| CB | CB | ILE- 200 | 3.61 | 0 | Hydrophobic |
| N | OG | SER- 201 | 3.28 | 170.11 | H-Bond (Ligand Donor) |
| CB | CB | SER- 201 | 4.21 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 250 | 2.97 | 177.8 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 250 | 3.3 | 127.02 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 250 | 3.17 | 136.16 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 251 | 3.34 | 135.63 | H-Bond (Protein Donor) |
| SD | CE | MET- 255 | 3.92 | 0 | Hydrophobic |
| C3' | CE | MET- 255 | 4.14 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 277 | 2.83 | 160.52 | H-Bond (Ligand Donor) |
| N1 | N | ALA- 278 | 3.16 | 174.52 | H-Bond (Protein Donor) |
| C1' | SG | CYS- 296 | 3.86 | 0 | Hydrophobic |
| C5' | CB | CYS- 296 | 4.46 | 0 | Hydrophobic |
