sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.070 Å
X-ray
2012-05-14
| Name: | Histone-lysine N-methyltransferase KMT5C |
|---|---|
| ID: | KMT5C_MOUSE |
| AC: | Q6Q783 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 2.1.1.43 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 94 % |
| C | 6 % |
| B-Factor: | 28.454 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.712 | 776.250 |
| % Hydrophobic | % Polar |
|---|---|
| 40.43 | 59.57 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 74.36 % |
| 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 |
|---|---|---|
| -20.4624 | -7.85015 | 31.6465 |
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- 114 | 4.07 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 114 | 3.77 | 0 | Aromatic Face/Face |
| N | OE2 | GLU- 117 | 2.95 | 131.48 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 117 | 3.17 | 168.75 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 117 | 2.95 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 117 | 3.17 | 0 | Ionic (Ligand Cationic) |
| N | O | ALA- 121 | 2.88 | 170.42 | H-Bond (Ligand Donor) |
| O | N | ALA- 121 | 2.75 | 154.7 | H-Bond (Protein Donor) |
| C4' | CB | PHE- 160 | 4.29 | 0 | Hydrophobic |
| SD | CB | PHE- 160 | 3.97 | 0 | Hydrophobic |
| CB | CD1 | PHE- 180 | 4.28 | 0 | Hydrophobic |
| N | OD1 | ASN- 182 | 2.71 | 156.68 | H-Bond (Ligand Donor) |
| N7 | N | HIS- 183 | 3.06 | 165.16 | H-Bond (Protein Donor) |
| N6 | O | HIS- 183 | 2.92 | 156.74 | H-Bond (Ligand Donor) |
| C5' | CE2 | TYR- 217 | 3.97 | 0 | Hydrophobic |
| C3' | CE1 | PHE- 221 | 4.25 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 222 | 3.99 | 0 | Aromatic Edge/Face |
| C2' | CE1 | PHE- 222 | 4.03 | 0 | Hydrophobic |
| N1 | N | GLU- 230 | 3 | 153.94 | H-Bond (Protein Donor) |
