sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2004-12-06
| Name: | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase |
|---|---|
| ID: | MTNN_ECOLI |
| AC: | P0AF12 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 3.2.2.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 89 % |
| B | 11 % |
| B-Factor: | 26.582 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.100 | 280.125 |
| % Hydrophobic | % Polar |
|---|---|
| 69.88 | 30.12 |
| According to VolSite | |
| HET Code: | TDI |
|---|---|
| Formula: | C13H20N5OS |
| Molecular weight: | 294.396 g/mol |
| DrugBank ID: | DB08606 |
| Buried Surface Area: | 84.06 % |
| Polar Surface area: | 117.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 56.3158 | 73.0299 | 20.8522 |
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 |
| C4' | SD | MET- 9 | 3.77 | 0 | Hydrophobic |
| C3' | CG2 | ILE- 50 | 3.81 | 0 | Hydrophobic |
| CS5 | CD1 | ILE- 50 | 3.77 | 0 | Hydrophobic |
| S | CG1 | VAL- 102 | 3.85 | 0 | Hydrophobic |
| S | CE1 | PHE- 105 | 4.03 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 151 | 3.48 | 0 | Hydrophobic |
| S | CD2 | PHE- 151 | 4.11 | 0 | Hydrophobic |
| N6 | O | ILE- 152 | 2.91 | 146.32 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 152 | 2.89 | 147.01 | H-Bond (Protein Donor) |
| C3' | SD | MET- 173 | 3.58 | 0 | Hydrophobic |
| S | SD | MET- 173 | 4.11 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 174 | 2.78 | 163.88 | H-Bond (Ligand Donor) |
| N7 | OD2 | ASP- 197 | 2.77 | 156.9 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 197 | 3 | 162.32 | H-Bond (Ligand Donor) |
| CS5 | CE1 | PHE- 207 | 4.44 | 0 | Hydrophobic |
| C4' | CZ | PHE- 207 | 4.13 | 0 | Hydrophobic |
| N1' | O | HOH- 418 | 2.75 | 171.2 | H-Bond (Ligand Donor) |
