sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2013-02-14
| Name: | Histone-lysine N-methyltransferase SETD7 |
|---|---|
| ID: | SETD7_HUMAN |
| AC: | Q8WTS6 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.43 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 29.820 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.581 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 27.50 | 72.50 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 61.8 % |
| 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 |
|---|---|---|
| 54.5034 | -18.3777 | -9.23593 |
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 | GLU- 228 | 2.79 | 172.87 | H-Bond (Ligand Donor) |
| O | N | GLU- 228 | 2.84 | 145.65 | H-Bond (Protein Donor) |
| O | NZ | LYS- 294 | 3.66 | 0 | Ionic (Protein Cationic) |
| OXT | NZ | LYS- 294 | 2.72 | 0 | Ionic (Protein Cationic) |
| OXT | NZ | LYS- 294 | 2.72 | 149.58 | H-Bond (Protein Donor) |
| CB | CD | LYS- 294 | 4.39 | 0 | Hydrophobic |
| N | OD1 | ASN- 296 | 2.94 | 142.43 | H-Bond (Ligand Donor) |
| N7 | N | HIS- 297 | 2.97 | 170.19 | H-Bond (Protein Donor) |
| N6 | O | HIS- 297 | 3.05 | 148.09 | H-Bond (Ligand Donor) |
| CE | CZ | TYR- 335 | 4.23 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 335 | 4.25 | 0 | Hydrophobic |
| C3' | CZ2 | TRP- 352 | 3.98 | 0 | Hydrophobic |
| C2' | CE2 | TRP- 352 | 3.78 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 352 | 3.8 | 0 | Aromatic Face/Face |
| N6 | OE1 | GLU- 356 | 2.97 | 161.64 | H-Bond (Ligand Donor) |
| OXT | O | HOH- 545 | 2.7 | 179.96 | H-Bond (Protein Donor) |
