sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2010-01-11
| Name: | 16S rRNA (guanine(1405)-N(7))-methyltransferase |
|---|---|
| ID: | SGM_MICZI |
| AC: | Q7M0R2 |
| Organism: | Micromonospora zionensis |
| Reign: | Bacteria |
| TaxID: | 1879 |
| EC Number: | 2.1.1.179 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 25.137 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 6 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.898 | 462.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.91 | 51.09 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 76.01 % |
| 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 |
|---|---|---|
| 8.82189 | 1.60578 | 18.9009 |
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 |
| CE | CZ | PHE- 64 | 3.45 | 0 | Hydrophobic |
| C3' | CD2 | PHE- 64 | 4.08 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 64 | 3.98 | 0 | Hydrophobic |
| O3' | NE2 | HIS- 102 | 3.18 | 152.63 | H-Bond (Protein Donor) |
| CG | CB | SER- 104 | 3.56 | 0 | Hydrophobic |
| SD | CB | SER- 104 | 3.93 | 0 | Hydrophobic |
| O | NH1 | ARG- 108 | 3.27 | 155.54 | H-Bond (Protein Donor) |
| O | NH2 | ARG- 108 | 3.41 | 147.17 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 108 | 2.66 | 147.04 | H-Bond (Protein Donor) |
| O | CZ | ARG- 108 | 3.8 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 108 | 3.64 | 0 | Ionic (Protein Cationic) |
| N | O | ALA- 133 | 2.83 | 162.77 | H-Bond (Ligand Donor) |
| C4' | CB | ALA- 133 | 4.29 | 0 | Hydrophobic |
| C1' | CB | ALA- 133 | 3.68 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 156 | 3.18 | 153.6 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 156 | 2.57 | 158.39 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 182 | 3.09 | 154.84 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 183 | 2.98 | 154.9 | H-Bond (Protein Donor) |
| N | O | LEU- 198 | 3.18 | 166.82 | H-Bond (Ligand Donor) |
| CG | CB | LYS- 199 | 4.1 | 0 | Hydrophobic |
| CE | CB | LYS- 199 | 4.13 | 0 | Hydrophobic |
| N7 | NE2 | GLN- 207 | 3.01 | 161.45 | H-Bond (Protein Donor) |
| N6 | OE1 | GLN- 207 | 3.37 | 165.75 | H-Bond (Ligand Donor) |
| N | O | HOH- 275 | 2.59 | 148.8 | H-Bond (Ligand Donor) |
| OXT | O | HOH- 312 | 2.94 | 171.98 | H-Bond (Protein Donor) |
| O2' | O | HOH- 317 | 3.39 | 152.73 | H-Bond (Protein Donor) |
