sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.060 Å
X-ray
2012-09-10
| Name: | Histone-lysine N-methyltransferase SETD2 |
|---|---|
| ID: | SETD2_HUMAN |
| AC: | Q9BYW2 |
| 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: | 34.978 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.880 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 38.65 | 61.35 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 83.68 % |
| 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 |
|---|---|---|
| -2.672 | 28.5432 | 18.0752 |
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 | LYS- 1560 | 2.74 | 139.73 | H-Bond (Ligand Donor) |
| N | O | TRP- 1562 | 2.75 | 141.05 | H-Bond (Ligand Donor) |
| OXT | N | TRP- 1562 | 2.79 | 141.75 | H-Bond (Protein Donor) |
| SD | CB | HIS- 1603 | 4.37 | 0 | Hydrophobic |
| C4' | CB | HIS- 1603 | 3.8 | 0 | Hydrophobic |
| O2' | ND1 | HIS- 1603 | 2.71 | 164.69 | H-Bond (Ligand Donor) |
| O3' | N | TYR- 1604 | 3.06 | 167.33 | H-Bond (Protein Donor) |
| SD | CE1 | TYR- 1605 | 3.46 | 0 | Hydrophobic |
| CB | CE1 | TYR- 1605 | 4.04 | 0 | Hydrophobic |
| O | OH | TYR- 1605 | 2.62 | 153.24 | H-Bond (Protein Donor) |
| CB | CD1 | PHE- 1626 | 4.23 | 0 | Hydrophobic |
| N | OD1 | ASN- 1628 | 2.65 | 161.79 | H-Bond (Ligand Donor) |
| N7 | N | HIS- 1629 | 2.94 | 164.13 | H-Bond (Protein Donor) |
| N6 | O | HIS- 1629 | 3.06 | 156.03 | H-Bond (Ligand Donor) |
| C5' | CE1 | TYR- 1666 | 3.74 | 0 | Hydrophobic |
| C3' | CE1 | TYR- 1666 | 4.48 | 0 | Hydrophobic |
| O3' | OE1 | GLN- 1676 | 2.81 | 157.19 | H-Bond (Ligand Donor) |
| O2' | NE2 | GLN- 1676 | 3.02 | 127.5 | H-Bond (Protein Donor) |
| N1 | N | PHE- 1679 | 2.98 | 171.9 | H-Bond (Protein Donor) |
| C3' | CD1 | LEU- 1689 | 4.1 | 0 | Hydrophobic |
