sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2011-02-25
| Name: | 5-cytosine DNA methyltransferase |
|---|---|
| ID: | Q6Q386_ENTHI |
| AC: | Q6Q386 |
| Organism: | Entamoeba histolytica |
| Reign: | Eukaryota |
| TaxID: | 5759 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.759 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.975 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 37.64 | 62.36 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 66.49 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 19.235 | -22.8583 | 20.5658 |
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 |
| C1' | CD1 | PHE- 12 | 3.82 | 0 | Hydrophobic |
| C4' | CB | PHE- 12 | 3.69 | 0 | Hydrophobic |
| O | N | ILE- 15 | 2.85 | 179 | H-Bond (Protein Donor) |
| OXT | N | GLY- 17 | 2.93 | 126.06 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 37 | 2.97 | 165.75 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 37 | 2.66 | 155.62 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASN- 58 | 2.95 | 147.22 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 59 | 3.27 | 166.69 | H-Bond (Protein Donor) |
| N | OG | SER- 78 | 2.59 | 122.31 | H-Bond (Ligand Donor) |
| CG | CB | SER- 78 | 4.39 | 0 | Hydrophobic |
| SD | CB | ASN- 302 | 4.41 | 0 | Hydrophobic |
| N | O | HOH- 440 | 2.94 | 154.61 | H-Bond (Ligand Donor) |
