sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.300 Å
X-ray
2010-03-16
| Name: | Ribosomal RNA small subunit methyltransferase F |
|---|---|
| ID: | RSMF_THET8 |
| AC: | Q5SII2 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 12.749 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.612 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 45.73 | 54.27 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 57.57 % |
| 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 |
|---|---|---|
| -21.995 | -6.79048 | 11.8492 |
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 |
| N | O | ALA- 109 | 3 | 144.37 | H-Bond (Ligand Donor) |
| C1' | CB | ALA- 109 | 4 | 0 | Hydrophobic |
| C4' | CB | ALA- 109 | 3.68 | 0 | Hydrophobic |
| O | N | GLY- 113 | 2.98 | 149.94 | H-Bond (Protein Donor) |
| O | N | GLY- 114 | 2.93 | 153.64 | H-Bond (Protein Donor) |
| OXT | N | LYS- 115 | 3.04 | 149.91 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 115 | 2.99 | 125.37 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 115 | 2.99 | 0 | Ionic (Protein Cationic) |
| O3' | OE1 | GLU- 133 | 2.8 | 134.57 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 133 | 2.61 | 132.68 | H-Bond (Ligand Donor) |
| C2' | CD | ARG- 138 | 4.25 | 0 | Hydrophobic |
| N | OD2 | ASP- 177 | 2.83 | 152.29 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 177 | 2.83 | 0 | Ionic (Ligand Cationic) |
| CG | CB | ASP- 177 | 4.46 | 0 | Hydrophobic |
| C5' | CB | PRO- 179 | 4.19 | 0 | Hydrophobic |
| N | O | HOH- 869 | 2.98 | 151.84 | H-Bond (Ligand Donor) |
