sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
1998-09-03
| Name: | Modification methylase DpnIIA |
|---|---|
| ID: | MTD21_STREE |
| AC: | P04043 |
| Organism: | Streptococcus pneumoniae |
| Reign: | Bacteria |
| TaxID: | 1313 |
| EC Number: | 2.1.1.72 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.848 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.088 | 1036.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.60 | 54.40 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 69.52 % |
| 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 |
|---|---|---|
| 19.1244 | 31.0772 | 52.6496 |
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- 17 | 3.06 | 150.62 | H-Bond (Protein Donor) |
| O | N | LYS- 21 | 3.09 | 151.49 | H-Bond (Protein Donor) |
| C1' | CD2 | PHE- 43 | 4.06 | 0 | Hydrophobic |
| C4' | CB | PHE- 43 | 3.91 | 0 | Hydrophobic |
| OXT | N | GLY- 46 | 2.84 | 137.56 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 62 | 2.63 | 141.14 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 62 | 2.74 | 165.03 | H-Bond (Ligand Donor) |
| N3 | N | PHE- 63 | 3.45 | 136 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 177 | 3.17 | 172 | H-Bond (Ligand Donor) |
| N1 | N | PHE- 178 | 3.01 | 146 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 194 | 2.69 | 159.15 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 194 | 2.69 | 0 | Ionic (Ligand Cationic) |
| C5' | CG | PRO- 196 | 4.2 | 0 | Hydrophobic |
