sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 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: | 44.217 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.793 | 823.500 |
| % Hydrophobic | % Polar |
|---|---|
| 40.98 | 59.02 |
| According to VolSite | |
| HET Code: | SFG |
|---|---|
| Formula: | C15H24N7O5 |
| Molecular weight: | 382.395 g/mol |
| DrugBank ID: | DB01910 |
| Buried Surface Area: | 69.52 % |
| Polar Surface area: | 214.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -1.57741 | -1.17652 | 90.4228 |
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 | 2.92 | 164.45 | H-Bond (Protein Donor) |
| NE | O | ALA- 11 | 3.15 | 155.53 | H-Bond (Ligand Donor) |
| OXT | N | LYS- 14 | 3.37 | 156.91 | H-Bond (Protein Donor) |
| CG | CB | PHE- 35 | 4.42 | 0 | Hydrophobic |
| C1' | CD2 | PHE- 35 | 4.23 | 0 | Hydrophobic |
| C4' | CB | PHE- 35 | 3.83 | 0 | Hydrophobic |
| O | N | ALA- 38 | 2.74 | 142.32 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 54 | 2.86 | 170.08 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 54 | 2.76 | 168.67 | H-Bond (Ligand Donor) |
| C1' | CG2 | ILE- 55 | 4.3 | 0 | Hydrophobic |
| N6 | OG | SER- 164 | 3.06 | 156.41 | H-Bond (Ligand Donor) |
| N1 | N | TYR- 165 | 3.18 | 120.77 | H-Bond (Protein Donor) |
| CG | CB | ASP- 181 | 4.36 | 0 | Hydrophobic |
| NE | OD2 | ASP- 181 | 3.97 | 0 | Ionic (Ligand Cationic) |
| C5' | CG | PRO- 183 | 4.48 | 0 | Hydrophobic |
| N | O | HOH- 414 | 2.84 | 171.96 | H-Bond (Ligand Donor) |
