sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.120 Å
X-ray
2014-07-09
| Name: | 18S rRNA (guanine(1575)-N(7))-methyltransferase |
|---|---|
| ID: | BUD23_YEAST |
| AC: | P25627 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 34.047 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.006 | 651.375 |
| % Hydrophobic | % Polar |
|---|---|
| 51.81 | 48.19 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 73.27 % |
| 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 |
|---|---|---|
| 19.6309 | -13.056 | 37.3236 |
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 |
| C3' | CE2 | TYR- 14 | 3.85 | 0 | Hydrophobic |
| O | OH | TYR- 22 | 2.78 | 172.4 | H-Bond (Protein Donor) |
| CE | CZ | TYR- 22 | 3.83 | 0 | Hydrophobic |
| SD | CZ | TYR- 22 | 4.05 | 0 | Hydrophobic |
| OXT | NE2 | GLN- 32 | 2.66 | 163.28 | H-Bond (Protein Donor) |
| N | O | GLY- 55 | 2.9 | 157.37 | H-Bond (Ligand Donor) |
| N | OG | SER- 61 | 3.05 | 156.63 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 77 | 2.62 | 167.65 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 77 | 3.22 | 148.8 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 78 | 3.3 | 139.05 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 99 | 2.79 | 141.85 | H-Bond (Ligand Donor) |
| N1 | N | MET- 100 | 2.9 | 173.63 | H-Bond (Protein Donor) |
| N | O | ILE- 117 | 3.23 | 167.97 | H-Bond (Ligand Donor) |
| CG | CB | SER- 118 | 4.28 | 0 | Hydrophobic |
| CE | CB | SER- 118 | 4.06 | 0 | Hydrophobic |
| C4' | CB | ALA- 119 | 4.32 | 0 | Hydrophobic |
| O | O | HOH- 406 | 2.73 | 179.97 | H-Bond (Protein Donor) |
