sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.820 Å
X-ray
2013-12-20
| Name: | N-lysine methyltransferase SMYD2 |
|---|---|
| ID: | SMYD2_HUMAN |
| AC: | Q9NRG4 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 19.957 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.604 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 41.51 | 58.49 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 70.02 % |
| 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 |
|---|---|---|
| 57.1928 | 168.378 | -7.627 |
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 | ARG- 19 | 2.92 | 142.5 | H-Bond (Ligand Donor) |
| O | N | ARG- 19 | 2.67 | 151.32 | H-Bond (Protein Donor) |
| O | NE | ARG- 19 | 2.99 | 161.78 | H-Bond (Protein Donor) |
| OXT | NE | ARG- 19 | 3.05 | 137.11 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 19 | 2.8 | 148.18 | H-Bond (Protein Donor) |
| O | CZ | ARG- 19 | 3.91 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 19 | 3.34 | 0 | Ionic (Protein Cationic) |
| O2' | NE2 | HIS- 137 | 2.83 | 134.59 | H-Bond (Protein Donor) |
| N | OD1 | ASN- 206 | 2.99 | 150.8 | H-Bond (Ligand Donor) |
| N7 | N | HIS- 207 | 3.02 | 173.69 | H-Bond (Protein Donor) |
| N6 | O | HIS- 207 | 2.71 | 131.33 | H-Bond (Ligand Donor) |
| C5' | CE2 | TYR- 240 | 3.82 | 0 | Hydrophobic |
| C3' | CB | TYR- 258 | 4.16 | 0 | Hydrophobic |
| O3' | O | TYR- 258 | 2.55 | 175.98 | H-Bond (Ligand Donor) |
| DuAr | DuAr | PHE- 260 | 3.6 | 0 | Aromatic Face/Face |
| C2' | CD1 | PHE- 260 | 3.61 | 0 | Hydrophobic |
