sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.720 Å
X-ray
2016-04-22
| Name: | Histone-lysine N-methyltransferase EHMT2 |
|---|---|
| ID: | EHMT2_HUMAN |
| AC: | Q96KQ7 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 28.564 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.736 | 816.750 |
| % Hydrophobic | % Polar |
|---|---|
| 37.19 | 62.81 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 68.38 % |
| 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 |
|---|---|---|
| 56.5765 | -0.403889 | 101.079 |
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 |
| N | O | TRP- 1050 | 2.97 | 169.12 | H-Bond (Ligand Donor) |
| OXT | N | TRP- 1050 | 2.97 | 170.96 | H-Bond (Protein Donor) |
| C3' | CB | SER- 1084 | 4.42 | 0 | Hydrophobic |
| C4' | CB | SER- 1084 | 4.32 | 0 | Hydrophobic |
| O | OH | TYR- 1085 | 2.83 | 153.08 | H-Bond (Protein Donor) |
| SD | CE1 | TYR- 1085 | 3.43 | 0 | Hydrophobic |
| CE | CD1 | TYR- 1085 | 3.5 | 0 | Hydrophobic |
| CG | CE1 | TYR- 1085 | 4.37 | 0 | Hydrophobic |
| CB | CD1 | PHE- 1110 | 4.48 | 0 | Hydrophobic |
| N | OD1 | ASN- 1112 | 2.9 | 142.59 | H-Bond (Ligand Donor) |
| N7 | N | HIS- 1113 | 3.06 | 166.45 | H-Bond (Protein Donor) |
| N6 | O | HIS- 1113 | 2.81 | 139.24 | H-Bond (Ligand Donor) |
| CE | CZ | TYR- 1154 | 4.26 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 1154 | 3.86 | 0 | Hydrophobic |
| C3' | CZ | PHE- 1158 | 4.23 | 0 | Hydrophobic |
| C2' | CZ | PHE- 1166 | 3.69 | 0 | Hydrophobic |
| N1 | N | GLN- 1169 | 3 | 163.94 | H-Bond (Protein Donor) |
