sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2003-05-08
| Name: | 23S rRNA (guanine(745)-N(1))-methyltransferase |
|---|---|
| ID: | RLMA_ECOLI |
| AC: | P36999 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.147 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.319 | 972.000 |
| % Hydrophobic | % Polar |
|---|---|
| 52.78 | 47.22 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 53.74 % |
| 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 |
|---|---|---|
| 18.4235 | 28.4346 | 42.2893 |
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 |
| N | OH | TYR- 67 | 2.86 | 137.13 | H-Bond (Ligand Donor) |
| CB | CE2 | TYR- 67 | 3.76 | 0 | Hydrophobic |
| SD | CE2 | TYR- 67 | 4.27 | 0 | Hydrophobic |
| N1 | N | GLU- 96 | 3.25 | 133.59 | H-Bond (Protein Donor) |
| O4' | OH | TYR- 99 | 3.4 | 139.25 | H-Bond (Protein Donor) |
| C1' | CE1 | TYR- 99 | 4.4 | 0 | Hydrophobic |
| C5' | CG2 | ILE- 155 | 3.94 | 0 | Hydrophobic |
| CE | CD1 | TYR- 156 | 3.31 | 0 | Hydrophobic |
| C3' | CB | TYR- 156 | 3.44 | 0 | Hydrophobic |
| CG | CD1 | TYR- 156 | 4.07 | 0 | Hydrophobic |
| C5' | CB | TYR- 156 | 4.02 | 0 | Hydrophobic |
| CE | CB | PRO- 179 | 4.35 | 0 | Hydrophobic |
| SD | CE2 | PHE- 260 | 3.54 | 0 | Hydrophobic |
| CE | CD2 | PHE- 260 | 3.91 | 0 | Hydrophobic |
| N6 | O | HOH- 1434 | 2.69 | 135.41 | H-Bond (Ligand Donor) |
