sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2015-12-04
| Name: | Histone-lysine N-methyltransferase 2C |
|---|---|
| ID: | KMT2C_HUMAN |
| AC: | Q8NEZ4 |
| 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: | 32.516 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.154 | 847.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.83 | 58.17 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 62.53 % |
| 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 |
|---|---|---|
| -20.875 | 19.3987 | 5.52346 |
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 | OE1 | GLN- 4781 | 3.07 | 149.85 | H-Bond (Ligand Donor) |
| C1' | CB | GLN- 4781 | 4.42 | 0 | Hydrophobic |
| N | O | LEU- 4783 | 2.87 | 169.34 | H-Bond (Ligand Donor) |
| OXT | N | LEU- 4783 | 2.71 | 139.66 | H-Bond (Protein Donor) |
| SD | CE1 | TYR- 4825 | 3.55 | 0 | Hydrophobic |
| CB | CE1 | TYR- 4825 | 4.22 | 0 | Hydrophobic |
| O | OH | TYR- 4825 | 2.71 | 168.3 | H-Bond (Protein Donor) |
| CB | CD1 | TYR- 4846 | 3.98 | 0 | Hydrophobic |
| N7 | N | HIS- 4849 | 2.94 | 160.72 | H-Bond (Protein Donor) |
| N6 | O | HIS- 4849 | 2.73 | 143.78 | H-Bond (Ligand Donor) |
| C5' | CE2 | TYR- 4886 | 4.07 | 0 | Hydrophobic |
| N1 | N | HIS- 4900 | 2.86 | 159.88 | H-Bond (Protein Donor) |
| C2' | CE | MET- 4910 | 3.93 | 0 | Hydrophobic |
