sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2009-02-19
| Name: | tRNA (guanine(37)-N1)-methyltransferase Trm5b |
|---|---|
| ID: | TRM5B_METJA |
| AC: | Q58293 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | 2.1.1.228 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 48.200 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.922 | 1191.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.73 | 51.27 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 76.06 % |
| 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 |
|---|---|---|
| 10.6283 | -4.23478 | -6.53352 |
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 |
| CE | CG | ARG- 145 | 4.45 | 0 | Hydrophobic |
| C5' | CG | ARG- 145 | 3.9 | 0 | Hydrophobic |
| CE | CD2 | TYR- 177 | 3.52 | 0 | Hydrophobic |
| CB | CD2 | TYR- 177 | 3.71 | 0 | Hydrophobic |
| SD | CD2 | TYR- 177 | 3.61 | 0 | Hydrophobic |
| OXT | CZ | ARG- 186 | 3.45 | 0 | Ionic (Protein Cationic) |
| C1' | CB | PHE- 203 | 4.09 | 0 | Hydrophobic |
| C4' | CB | PHE- 203 | 3.77 | 0 | Hydrophobic |
| CA | CG | PRO- 208 | 3.96 | 0 | Hydrophobic |
| CA | CD1 | PHE- 209 | 4.33 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 223 | 2.85 | 151.05 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 223 | 2.95 | 141.73 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 223 | 2.62 | 157.08 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 224 | 2.94 | 147.24 | H-Bond (Protein Donor) |
| C1' | CG2 | ILE- 224 | 4.37 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 251 | 3.46 | 165.08 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 252 | 2.86 | 167.34 | H-Bond (Protein Donor) |
| C1' | CD1 | LEU- 266 | 4.46 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 266 | 3.82 | 0 | Hydrophobic |
| O3' | O | HOH- 506 | 2.71 | 154.24 | H-Bond (Protein Donor) |
