sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.390 Å
X-ray
2014-11-15
| Name: | DNA adenine methylase |
|---|---|
| ID: | DMA_ECOLI |
| AC: | P0AEE8 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 2.1.1.72 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.888 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.587 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 40.50 | 59.50 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 65.79 % |
| 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 |
|---|---|---|
| -24.8336 | -30.0955 | 151.371 |
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 |
| O3' | NE1 | TRP- 10 | 3.24 | 135.04 | H-Bond (Protein Donor) |
| SD | CB | PHE- 35 | 4.37 | 0 | Hydrophobic |
| C4' | CB | PHE- 35 | 4.5 | 0 | Hydrophobic |
| C1' | CD2 | PHE- 35 | 4.03 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 54 | 3.02 | 169.56 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 54 | 3.27 | 138.95 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 55 | 3.46 | 129.86 | H-Bond (Protein Donor) |
| C2' | CG2 | ILE- 55 | 4.05 | 0 | Hydrophobic |
| N1 | N | TYR- 165 | 3.09 | 124.55 | H-Bond (Protein Donor) |
| N | OD1 | ASP- 181 | 3.14 | 154.21 | H-Bond (Ligand Donor) |
| N | OD1 | ASP- 181 | 3.14 | 0 | Ionic (Ligand Cationic) |
| N | O | PRO- 182 | 3.23 | 154.9 | H-Bond (Ligand Donor) |
| C5' | CG | PRO- 183 | 4.3 | 0 | Hydrophobic |
| O | N | TYR- 184 | 2.88 | 154.12 | H-Bond (Protein Donor) |
