sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.450 Å
X-ray
2009-04-04
| Name: | 23S rRNA (adenosine(1067)-2'-O)-methyltransferase |
|---|---|
| ID: | TSNR_STRAJ |
| AC: | P18644 |
| Organism: | Streptomyces azureus |
| Reign: | Bacteria |
| TaxID: | 146537 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 94 % |
| B | 6 % |
| B-Factor: | 66.099 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.267 | 880.875 |
| % Hydrophobic | % Polar |
|---|---|
| 32.18 | 67.82 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 75.26 % |
| 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 |
|---|---|---|
| 13.1786 | 29.8953 | 80.8551 |
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 |
| OXT | NH1 | ARG- 135 | 2.65 | 122.97 | H-Bond (Protein Donor) |
| OXT | CZ | ARG- 135 | 3.65 | 0 | Ionic (Protein Cationic) |
| OXT | NH1 | ARG- 165 | 2.95 | 142.68 | H-Bond (Protein Donor) |
| OXT | CZ | ARG- 165 | 3.79 | 0 | Ionic (Protein Cationic) |
| O2' | O | LEU- 195 | 2.52 | 171.06 | H-Bond (Ligand Donor) |
| C1' | CD1 | PHE- 217 | 4.1 | 0 | Hydrophobic |
| O2' | N | GLY- 218 | 3.44 | 157.41 | H-Bond (Protein Donor) |
| CE | CB | LYS- 221 | 3.8 | 0 | Hydrophobic |
| N6 | O | ILE- 238 | 3.2 | 158.97 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 238 | 2.63 | 159.35 | H-Bond (Protein Donor) |
| CE | CB | SER- 246 | 3.9 | 0 | Hydrophobic |
| N7 | OG | SER- 246 | 2.88 | 138.1 | H-Bond (Protein Donor) |
| N7 | N | LEU- 247 | 3.19 | 159.49 | H-Bond (Protein Donor) |
| C4' | CB | VAL- 249 | 4.05 | 0 | Hydrophobic |
| O4' | OG | SER- 252 | 3.35 | 140.24 | H-Bond (Protein Donor) |
| C1' | CB | SER- 252 | 3.76 | 0 | Hydrophobic |
