sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.100 Å
X-ray
2014-01-22
| Name: | SpoU rRNA methylase |
|---|---|
| ID: | Q4JB16_SULAC |
| AC: | Q4JB16 |
| Organism: | Sulfolobus acidocaldarius |
| Reign: | Archaea |
| TaxID: | 330779 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 14.762 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.248 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 31.75 | 68.25 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 69.54 % |
| 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 |
|---|---|---|
| -45.2461 | -26.9822 | 149.474 |
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 |
| C2' | CB | THR- 77 | 4.16 | 0 | Hydrophobic |
| O2' | OG1 | THR- 77 | 2.63 | 170.67 | H-Bond (Ligand Donor) |
| C1' | CD2 | PHE- 110 | 4.29 | 0 | Hydrophobic |
| O3' | N | GLY- 111 | 3.15 | 122.59 | H-Bond (Protein Donor) |
| O2' | N | GLY- 111 | 3.05 | 162.71 | H-Bond (Protein Donor) |
| N | O | SER- 114 | 3.35 | 149.85 | H-Bond (Ligand Donor) |
| N6 | O | ILE- 131 | 3.08 | 154.5 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 131 | 2.92 | 169 | H-Bond (Protein Donor) |
| N6 | O | PRO- 138 | 2.91 | 158.45 | H-Bond (Ligand Donor) |
| CB | CG1 | VAL- 139 | 3.85 | 0 | Hydrophobic |
| SD | CG1 | VAL- 139 | 3.9 | 0 | Hydrophobic |
| N7 | N | LEU- 140 | 2.99 | 155.45 | H-Bond (Protein Donor) |
| C5' | CB | LEU- 142 | 4.28 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 142 | 4.07 | 0 | Hydrophobic |
| C1' | CB | ALA- 145 | 3.78 | 0 | Hydrophobic |
