sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2008-10-21
| Name: | Probable ribosomal RNA small subunit methyltransferase |
|---|---|
| ID: | Q5SKW0_THET8 |
| AC: | Q5SKW0 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 15.213 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.832 | 742.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.18 | 56.82 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 69.18 % |
| 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 |
|---|---|---|
| 28.5796 | 14.0546 | 18.802 |
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 |
| SD | CD2 | PHE- 207 | 3.3 | 0 | Hydrophobic |
| CE | CZ | PHE- 207 | 3.51 | 0 | Hydrophobic |
| C3' | CB | PHE- 207 | 4.38 | 0 | Hydrophobic |
| OXT | OG | SER- 216 | 2.57 | 156.9 | H-Bond (Protein Donor) |
| N | O | GLY- 241 | 2.76 | 165.1 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 262 | 3.33 | 126.09 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 262 | 2.54 | 154.37 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 262 | 2.61 | 161.5 | H-Bond (Ligand Donor) |
| N3 | N | ASP- 263 | 3.28 | 144.14 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 288 | 3.07 | 157.15 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 289 | 2.88 | 154.46 | H-Bond (Protein Donor) |
| C5' | CB | PRO- 307 | 4.27 | 0 | Hydrophobic |
| CE | CE2 | PHE- 308 | 4.35 | 0 | Hydrophobic |
| N6 | O | HOH- 378 | 3.06 | 127.72 | H-Bond (Ligand Donor) |
| O3' | O | HOH- 380 | 2.86 | 168.4 | H-Bond (Protein Donor) |
| N | O | HOH- 394 | 2.98 | 167.05 | H-Bond (Ligand Donor) |
