sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.170 Å
X-ray
2013-06-21
| Name: | Histone-lysine N-methyltransferase KMT5B |
|---|---|
| ID: | KMT5B_MOUSE |
| AC: | Q3U8K7 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 2.1.1.43 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.854 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.979 | 961.875 |
| % Hydrophobic | % Polar |
|---|---|
| 37.54 | 62.46 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 77.72 % |
| 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 |
|---|---|---|
| 8.27 | 48.7954 | 6.97344 |
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 |
| C1' | CD2 | TYR- 195 | 3.94 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 195 | 3.93 | 0 | Aromatic Face/Face |
| O2' | OG | SER- 197 | 2.72 | 165.09 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 198 | 3.19 | 129.92 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 198 | 2.77 | 160.52 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 198 | 3.19 | 0 | Ionic (Ligand Cationic) |
| N | OE2 | GLU- 198 | 2.77 | 0 | Ionic (Ligand Cationic) |
| N | O | ALA- 202 | 3.09 | 160.03 | H-Bond (Ligand Donor) |
| O | N | ALA- 202 | 2.81 | 143.38 | H-Bond (Protein Donor) |
| SD | CD1 | PHE- 242 | 4.41 | 0 | Hydrophobic |
| C4' | CB | PHE- 242 | 4.43 | 0 | Hydrophobic |
| CE | CB | SER- 243 | 3.92 | 0 | Hydrophobic |
| N | OD1 | ASN- 264 | 2.82 | 147.23 | H-Bond (Ligand Donor) |
| N7 | N | HIS- 265 | 3.1 | 161.64 | H-Bond (Protein Donor) |
| N6 | O | HIS- 265 | 2.91 | 147.74 | H-Bond (Ligand Donor) |
| CE | CZ | TYR- 299 | 3.84 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 299 | 3.73 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 304 | 3.99 | 0 | Aromatic Face/Face |
| C3' | CE1 | PHE- 304 | 4.11 | 0 | Hydrophobic |
| N1 | N | GLU- 312 | 3 | 165.26 | H-Bond (Protein Donor) |
| N3 | O | HOH- 2050 | 2.9 | 179.95 | H-Bond (Protein Donor) |
