sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2006-12-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.240 | 6.240 | 6.240 | 0.000 | 6.240 | 1 |
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 21.307 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.618 | 891.000 |
| % Hydrophobic | % Polar |
|---|---|
| 35.98 | 64.02 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 67.95 % |
| 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 |
|---|---|---|
| 37.6783 | 89.0187 | 82.4832 |
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 | 2.74 | 131.37 | H-Bond (Ligand Donor) |
| OXT | N | TRP- 1050 | 2.84 | 153.35 | H-Bond (Protein Donor) |
| CB | CE1 | TYR- 1085 | 4.43 | 0 | Hydrophobic |
| SD | CE1 | TYR- 1085 | 3.58 | 0 | Hydrophobic |
| O | OH | TYR- 1085 | 2.76 | 154.28 | H-Bond (Protein Donor) |
| CB | CD1 | PHE- 1110 | 4.37 | 0 | Hydrophobic |
| N | OD1 | ASN- 1112 | 2.81 | 174.74 | H-Bond (Ligand Donor) |
| N7 | N | HIS- 1113 | 2.96 | 160.51 | H-Bond (Protein Donor) |
| N6 | O | HIS- 1113 | 2.87 | 143.61 | H-Bond (Ligand Donor) |
| C5' | CE2 | TYR- 1154 | 4.05 | 0 | Hydrophobic |
| C2' | CZ | PHE- 1166 | 3.75 | 0 | Hydrophobic |
| N1 | N | GLN- 1169 | 2.94 | 164.57 | H-Bond (Protein Donor) |
