sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.740 Å
X-ray
2015-10-11
| Name: | N2, N2-dimethylguanosine tRNA methyltransferase |
|---|---|
| ID: | Q5JID5_THEKO |
| AC: | Q5JID5 |
| Organism: | Thermococcus kodakarensis ) |
| Reign: | Archaea |
| TaxID: | 69014 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.697 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.542 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.97 | 48.03 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 69.4 % |
| 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 |
|---|---|---|
| -12.4954 | -8.2883 | 19.4527 |
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 |
| SD | CD1 | ILE- 163 | 3.88 | 0 | Hydrophobic |
| CE | CB | ILE- 163 | 4.17 | 0 | Hydrophobic |
| CG | CD1 | ILE- 163 | 4.47 | 0 | Hydrophobic |
| N | OD2 | ASP- 185 | 2.73 | 164.87 | H-Bond (Ligand Donor) |
| N | OD1 | ASP- 185 | 3.35 | 122.31 | H-Bond (Ligand Donor) |
| N | O | PHE- 187 | 2.95 | 129.59 | H-Bond (Ligand Donor) |
| C1' | CD1 | PHE- 187 | 4.38 | 0 | Hydrophobic |
| C4' | CB | PHE- 187 | 4.13 | 0 | Hydrophobic |
| O | N | ILE- 193 | 3.04 | 140.85 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 208 | 2.65 | 168.68 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 208 | 3.46 | 136.1 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 208 | 2.71 | 156.21 | H-Bond (Ligand Donor) |
| C1' | CG2 | ILE- 209 | 4.36 | 0 | Hydrophobic |
| N3 | N | ILE- 209 | 3.25 | 141.3 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 235 | 3.02 | 173.36 | H-Bond (Ligand Donor) |
| N1 | N | ALA- 236 | 2.85 | 170.25 | H-Bond (Protein Donor) |
| CA | CB | ASP- 254 | 4.49 | 0 | Hydrophobic |
| CG | CB | ASP- 254 | 4.36 | 0 | Hydrophobic |
| C5' | CB | PRO- 256 | 4.48 | 0 | Hydrophobic |
| O | O | HOH- 538 | 2.58 | 179.97 | H-Bond (Protein Donor) |
