sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.370 Å
X-ray
2014-10-02
| Name: | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase |
|---|---|
| ID: | MTNN_VIBC3 |
| AC: | A5F5R2 |
| Organism: | Vibrio cholerae serotype O1 |
| Reign: | Bacteria |
| TaxID: | 345073 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 89 % |
| B | 11 % |
| B-Factor: | 10.744 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.957 | 239.625 |
| % Hydrophobic | % Polar |
|---|---|
| 71.83 | 28.17 |
| According to VolSite | |
| HET Code: | TDI |
|---|---|
| Formula: | C13H20N5OS |
| Molecular weight: | 294.396 g/mol |
| DrugBank ID: | DB08606 |
| Buried Surface Area: | 85.36 % |
| 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 |
|---|---|---|
| 11.6609 | -7.86015 | 19.133 |
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 | 3.88 | 0 | Hydrophobic |
| CS5 | CD1 | ILE- 50 | 3.86 | 0 | Hydrophobic |
| S | CG2 | ILE- 50 | 4.21 | 0 | Hydrophobic |
| C3' | CG2 | ILE- 50 | 3.74 | 0 | Hydrophobic |
| S | CG1 | VAL- 102 | 4.06 | 0 | Hydrophobic |
| CS5 | CD2 | PHE- 105 | 3.81 | 0 | Hydrophobic |
| S | CE2 | PHE- 105 | 4.14 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 152 | 3.33 | 0 | Hydrophobic |
| C5' | CD1 | PHE- 152 | 3.67 | 0 | Hydrophobic |
| N6 | O | VAL- 153 | 2.92 | 158 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 153 | 2.95 | 156.93 | H-Bond (Protein Donor) |
| S | SD | MET- 174 | 3.95 | 0 | Hydrophobic |
| C3' | SD | MET- 174 | 3.67 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 175 | 2.73 | 176 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 175 | 3.5 | 131.52 | H-Bond (Ligand Donor) |
| N7 | OD1 | ASP- 198 | 2.76 | 162.35 | H-Bond (Ligand Donor) |
| N6 | OD2 | ASP- 198 | 2.93 | 161.86 | H-Bond (Ligand Donor) |
| CS5 | CE2 | PHE- 208 | 4.12 | 0 | Hydrophobic |
| C4' | CZ | PHE- 208 | 4 | 0 | Hydrophobic |
| N1' | O | HOH- 485 | 2.73 | 177.67 | H-Bond (Ligand Donor) |
