sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.930 Å
X-ray
2016-04-17
| Name: | Methyl transferase |
|---|---|
| ID: | Q9LBJ0_BURGL |
| AC: | Q9LBJ0 |
| Organism: | Burkholderia glumae |
| Reign: | Bacteria |
| TaxID: | 337 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.844 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.792 | 735.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.46 | 49.54 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 60.99 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 24.1386 | 36.8073 | 40.1072 |
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- 24 | 3.22 | 156.98 | H-Bond (Protein Donor) |
| N | O | ALA- 47 | 2.64 | 159.39 | H-Bond (Ligand Donor) |
| C4' | CB | ALA- 47 | 4.02 | 0 | Hydrophobic |
| C1' | CB | ALA- 47 | 3.92 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 69 | 3.39 | 128.16 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 69 | 2.68 | 168.04 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 69 | 2.59 | 158.2 | H-Bond (Ligand Donor) |
| C1' | CG2 | ILE- 70 | 4.48 | 0 | Hydrophobic |
| N3 | N | ILE- 70 | 3.11 | 141.73 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 95 | 2.9 | 140.04 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 96 | 2.98 | 179.43 | H-Bond (Protein Donor) |
| N | O | ALA- 111 | 2.84 | 149.46 | H-Bond (Ligand Donor) |
| CG | CB | TRP- 112 | 3.91 | 0 | Hydrophobic |
| C5' | CB | TRP- 112 | 4.41 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 116 | 3.69 | 0 | Hydrophobic |
| OXT | O | HOH- 545 | 3.26 | 179.97 | H-Bond (Protein Donor) |
