sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.590 Å
X-ray
2010-01-22
| Name: | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI |
|---|---|
| ID: | TRMI_PYRAB |
| AC: | Q9V1J7 |
| Organism: | Pyrococcus abyssi |
| Reign: | Archaea |
| TaxID: | 272844 |
| EC Number: | 2.1.1.219 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 43.535 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.508 | 570.375 |
| % Hydrophobic | % Polar |
|---|---|
| 44.97 | 55.03 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 57.48 % |
| 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 |
|---|---|---|
| -12.1168 | -26.7611 | -29.8096 |
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 |
| O3' | OE2 | GLU- 125 | 2.79 | 150.67 | H-Bond (Ligand Donor) |
| O2' | OE1 | GLU- 125 | 2.58 | 155.45 | H-Bond (Ligand Donor) |
| C3' | CD1 | PHE- 130 | 4.22 | 0 | Hydrophobic |
| N6 | OD2 | ASP- 153 | 2.67 | 128.25 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 154 | 3.12 | 152.54 | H-Bond (Protein Donor) |
| SD | CG | PRO- 171 | 4.38 | 0 | Hydrophobic |
