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
2016-01-21
| Name: | Histone-lysine N-methyltransferase SMYD3 |
|---|---|
| ID: | SMYD3_HUMAN |
| AC: | Q9H7B4 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.43 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 97 % |
| J | 3 % |
| B-Factor: | 29.147 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.212 | 408.375 |
| % Hydrophobic | % Polar |
|---|---|
| 31.40 | 68.60 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 71.87 % |
| 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 |
|---|---|---|
| -0.939654 | -35.4165 | -14.9988 |
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 | ASN- 16 | 3.04 | 140.33 | H-Bond (Ligand Donor) |
| O | N | ASN- 16 | 2.84 | 142.67 | H-Bond (Protein Donor) |
| OXT | OH | TYR- 124 | 2.64 | 142.63 | H-Bond (Protein Donor) |
| C4' | CG | GLU- 130 | 4.36 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 132 | 2.9 | 153.55 | H-Bond (Protein Donor) |
| C5' | SG | CYS- 180 | 3.83 | 0 | Hydrophobic |
| C4' | SG | CYS- 180 | 4.28 | 0 | Hydrophobic |
| N | OD1 | ASN- 205 | 2.96 | 169.27 | H-Bond (Ligand Donor) |
| N7 | N | HIS- 206 | 2.91 | 173.83 | H-Bond (Protein Donor) |
| N6 | O | HIS- 206 | 2.97 | 144.89 | H-Bond (Ligand Donor) |
| C5' | CE2 | TYR- 239 | 4.06 | 0 | Hydrophobic |
| C3' | CB | TYR- 257 | 4.17 | 0 | Hydrophobic |
| O3' | O | TYR- 257 | 2.64 | 161.89 | H-Bond (Ligand Donor) |
| DuAr | DuAr | PHE- 259 | 3.62 | 0 | Aromatic Face/Face |
| C2' | CD1 | PHE- 259 | 3.79 | 0 | Hydrophobic |
| N6 | O | HOH- 638 | 2.99 | 157.38 | H-Bond (Ligand Donor) |
| N1 | O | HOH- 642 | 2.64 | 179.96 | H-Bond (Protein Donor) |
