sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.890 Å
X-ray
2006-02-14
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 25.877 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.879 | 941.625 |
| % Hydrophobic | % Polar |
|---|---|
| 47.31 | 52.69 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 71.58 % |
| 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 |
|---|---|---|
| -2.85262 | -63.0218 | 15.8209 |
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 |
| C3' | CZ2 | TRP- 10 | 4.38 | 0 | Hydrophobic |
| O3' | NE1 | TRP- 10 | 3 | 140.22 | H-Bond (Protein Donor) |
| O | N | LYS- 14 | 3.04 | 153.37 | H-Bond (Protein Donor) |
| C1' | CD2 | PHE- 35 | 4 | 0 | Hydrophobic |
| C4' | CB | PHE- 35 | 3.93 | 0 | Hydrophobic |
| OXT | N | ALA- 38 | 3.01 | 129.39 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 54 | 2.77 | 175.15 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 54 | 2.63 | 165.19 | H-Bond (Ligand Donor) |
| C1' | CG2 | ILE- 55 | 4.35 | 0 | Hydrophobic |
| N3 | N | ILE- 55 | 3.34 | 140.34 | H-Bond (Protein Donor) |
| N6 | OG | SER- 164 | 3.07 | 159.58 | H-Bond (Ligand Donor) |
| N1 | N | TYR- 165 | 3.13 | 136.91 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 181 | 2.73 | 160.36 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 181 | 2.73 | 0 | Ionic (Ligand Cationic) |
| CG | CB | ASP- 181 | 4.15 | 0 | Hydrophobic |
| C5' | CG | PRO- 183 | 4.34 | 0 | Hydrophobic |
| N | O | HOH- 404 | 2.85 | 156.26 | H-Bond (Ligand Donor) |
