sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2011-07-14
| Name: | Putative methyltransferase |
|---|---|
| ID: | Q8A3I2_BACTN |
| AC: | Q8A3I2 |
| Organism: | Bacteroides thetaiotaomicron |
| Reign: | Bacteria |
| TaxID: | 226186 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 42.599 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.020 | 999.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.61 | 54.39 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 69.86 % |
| 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 |
|---|---|---|
| -16.5807 | -21.2266 | 13.0759 |
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 |
| O | NH2 | ARG- 25 | 3.08 | 173.08 | H-Bond (Protein Donor) |
| OXT | NE | ARG- 25 | 2.99 | 173.93 | H-Bond (Protein Donor) |
| O | CZ | ARG- 25 | 3.89 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 25 | 3.84 | 0 | Ionic (Protein Cationic) |
| OXT | N | GLN- 26 | 3.19 | 148.17 | H-Bond (Protein Donor) |
| SD | CB | GLN- 26 | 3.87 | 0 | Hydrophobic |
| CB | CB | GLN- 26 | 4 | 0 | Hydrophobic |
| N | O | GLY- 54 | 2.71 | 166.71 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 76 | 2.54 | 160.79 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 76 | 2.92 | 154.34 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 76 | 3.18 | 145.34 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 77 | 3.37 | 125.17 | H-Bond (Protein Donor) |
| C3' | CE2 | PHE- 81 | 4.3 | 0 | Hydrophobic |
| N | O | GLU- 121 | 2.85 | 152.01 | H-Bond (Ligand Donor) |
| C5' | CB | ALA- 123 | 4.11 | 0 | Hydrophobic |
| CE | CE2 | TYR- 125 | 3.97 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 125 | 4.3 | 0 | Hydrophobic |
