sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-05-22
| Name: | Ribosomal RNA large subunit methyltransferase H |
|---|---|
| ID: | RLMH_STAAU |
| AC: | P0C1V0 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 1280 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.319 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.508 | 364.500 |
| % Hydrophobic | % Polar |
|---|---|
| 46.30 | 53.70 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 67.56 % |
| 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 |
|---|---|---|
| -5.50904 | -9.0423 | 4.75185 |
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 |
| O2' | O | LEU- 76 | 2.63 | 169.42 | H-Bond (Ligand Donor) |
| C2' | CB | LEU- 76 | 4.24 | 0 | Hydrophobic |
| CB | CD1 | ILE- 78 | 4.22 | 0 | Hydrophobic |
| C4' | CG2 | ILE- 107 | 4 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 107 | 3.98 | 0 | Hydrophobic |
| O2' | N | GLY- 108 | 3.2 | 165.03 | H-Bond (Protein Donor) |
| N1 | N | PHE- 127 | 2.96 | 176.29 | H-Bond (Protein Donor) |
| N6 | O | SER- 128 | 2.95 | 135.7 | H-Bond (Ligand Donor) |
| N6 | O | MET- 130 | 2.69 | 143.84 | H-Bond (Ligand Donor) |
| CB | CG2 | THR- 131 | 4.47 | 0 | Hydrophobic |
| CE | CG2 | THR- 131 | 3.83 | 0 | Hydrophobic |
| N7 | N | PHE- 132 | 3.06 | 166 | H-Bond (Protein Donor) |
| C5' | CB | HIS- 134 | 4.13 | 0 | Hydrophobic |
| C1' | CG | MET- 137 | 3.72 | 0 | Hydrophobic |
