sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 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 | 10 % |
| B | 90 % |
| B-Factor: | 23.333 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.376 | 705.375 |
| % Hydrophobic | % Polar |
|---|---|
| 34.45 | 65.55 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 74.01 % |
| 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 |
|---|---|---|
| 8.41623 | 3.61612 | 15.0952 |
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 |
| O | NH1 | ARG- 135 | 3.04 | 151.67 | H-Bond (Protein Donor) |
| O | CZ | ARG- 135 | 3.86 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 135 | 3.83 | 0 | Ionic (Protein Cationic) |
| O2' | O | LEU- 161 | 2.68 | 149.82 | H-Bond (Ligand Donor) |
| C2' | CB | LEU- 161 | 4.26 | 0 | Hydrophobic |
| C4' | CG1 | VAL- 184 | 4.44 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 184 | 4.43 | 0 | Hydrophobic |
| O2' | N | GLY- 185 | 2.94 | 165.85 | H-Bond (Protein Donor) |
| N | O | GLU- 187 | 3.13 | 161.13 | H-Bond (Ligand Donor) |
| N | O | GLY- 188 | 3.21 | 155.38 | H-Bond (Ligand Donor) |
| N6 | O | LEU- 208 | 3.18 | 161.06 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 208 | 2.77 | 165.31 | H-Bond (Protein Donor) |
| N6 | O | TYR- 211 | 2.98 | 137.42 | H-Bond (Ligand Donor) |
| SD | CG2 | THR- 212 | 4.46 | 0 | Hydrophobic |
| CB | CG2 | THR- 212 | 3.57 | 0 | Hydrophobic |
| N7 | N | LEU- 213 | 2.99 | 171.88 | H-Bond (Protein Donor) |
| C5' | CB | THR- 215 | 4.25 | 0 | Hydrophobic |
| C1' | CB | ALA- 218 | 3.7 | 0 | Hydrophobic |
