sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-04-30
| Name: | 16S rRNA (adenine(1408)-N(1))-methyltransferase |
|---|---|
| ID: | NPMA_ECOLX |
| AC: | A8C927 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | 2.1.1.180 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.125 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.602 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 51.41 | 48.59 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 69.84 % |
| 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 |
|---|---|---|
| 26.8648 | 16.2987 | 23.4392 |
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 | O | GLY- 32 | 2.8 | 162.77 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 55 | 3.39 | 120.8 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 55 | 2.63 | 158.28 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 55 | 2.9 | 153.19 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 55 | 3.48 | 151.01 | H-Bond (Ligand Donor) |
| C1' | CG | PRO- 56 | 4.5 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 60 | 3.4 | 121.67 | H-Bond (Protein Donor) |
| N1 | N | ALA- 87 | 2.87 | 173.43 | H-Bond (Protein Donor) |
| N6 | OE2 | GLU- 88 | 2.66 | 152 | H-Bond (Ligand Donor) |
| N | O | LEU- 104 | 2.72 | 154.2 | H-Bond (Ligand Donor) |
| CB | CB | PHE- 105 | 4.5 | 0 | Hydrophobic |
| CE | CE3 | TRP- 107 | 3.51 | 0 | Hydrophobic |
| C3' | CE2 | TRP- 107 | 4.22 | 0 | Hydrophobic |
| SD | CE2 | TRP- 107 | 3.77 | 0 | Hydrophobic |
| CE | CE2 | TRP- 197 | 3.86 | 0 | Hydrophobic |
| N | O | HOH- 233 | 2.86 | 168.81 | H-Bond (Ligand Donor) |
