sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-07-30
| Name: | Dimethyladenosine transferase 1, mitochondrial |
|---|---|
| ID: | TFB1M_MOUSE |
| AC: | Q8JZM0 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 2.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 41.696 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.561 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 54.46 | 45.54 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 80.6 % |
| 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 |
|---|---|---|
| -19.808 | -35.49 | -19.8128 |
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 |
| C5' | CG | GLN- 35 | 4.44 | 0 | Hydrophobic |
| CE | CB | GLN- 35 | 3.55 | 0 | Hydrophobic |
| SD | CD1 | PHE- 37 | 3.76 | 0 | Hydrophobic |
| O | N | LEU- 38 | 3.33 | 145.66 | H-Bond (Protein Donor) |
| OXT | N | LEU- 38 | 2.53 | 154.89 | H-Bond (Protein Donor) |
| O3' | OE1 | GLU- 85 | 3.41 | 151.01 | H-Bond (Ligand Donor) |
| N3 | N | LYS- 86 | 3.22 | 130.5 | H-Bond (Protein Donor) |
| C2' | CB | ASP- 87 | 4.45 | 0 | Hydrophobic |
| O2' | N | ASP- 87 | 3.42 | 138.55 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 111 | 2.74 | 164.69 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 112 | 2.88 | 170.4 | H-Bond (Protein Donor) |
| OXT | ND2 | ASN- 141 | 3.21 | 125.46 | H-Bond (Protein Donor) |
| N | O | HOH- 513 | 2.71 | 173.78 | H-Bond (Ligand Donor) |
