sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2007-03-02
| Name: | Ribosomal RNA small subunit methyltransferase E |
|---|---|
| ID: | RSME_AQUAE |
| AC: | O66552 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | 2.1.1.193 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 7 % |
| B | 93 % |
| B-Factor: | 13.386 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.578 | 934.875 |
| % Hydrophobic | % Polar |
|---|---|
| 35.38 | 64.62 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 71.97 % |
| 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 |
|---|---|---|
| 53.2282 | -9.4423 | 14.784 |
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 |
| O2' | O | LEU- 161 | 2.75 | 161.45 | H-Bond (Ligand Donor) |
| C2' | CB | LEU- 161 | 4.21 | 0 | Hydrophobic |
| CB | CZ | PHE- 164 | 4.3 | 0 | Hydrophobic |
| CG | CE2 | PHE- 164 | 4.28 | 0 | Hydrophobic |
| C4' | CG1 | VAL- 184 | 4.49 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 184 | 4.29 | 0 | Hydrophobic |
| O2' | N | GLY- 185 | 2.89 | 177.48 | H-Bond (Protein Donor) |
| N6 | O | LEU- 208 | 3.01 | 157.94 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 208 | 2.83 | 165.38 | H-Bond (Protein Donor) |
| N6 | O | TYR- 211 | 3.01 | 135.35 | H-Bond (Ligand Donor) |
| CB | CG2 | THR- 212 | 4.43 | 0 | Hydrophobic |
| SD | CG2 | THR- 212 | 4.18 | 0 | Hydrophobic |
| N7 | N | LEU- 213 | 2.96 | 171.46 | H-Bond (Protein Donor) |
| C5' | CB | THR- 215 | 4.34 | 0 | Hydrophobic |
| C1' | CB | ALA- 218 | 3.49 | 0 | Hydrophobic |
| O3' | O | HOH- 1401 | 2.74 | 168.75 | H-Bond (Ligand Donor) |
