sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.790 Å
X-ray
2013-05-12
| Name: | Aminodeoxyfutalosine nucleosidase |
|---|---|
| ID: | MQMTN_HELPY |
| AC: | O24915 |
| Organism: | Helicobacter pylori |
| Reign: | Bacteria |
| TaxID: | 85962 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 89 % |
| B | 11 % |
| B-Factor: | 24.888 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.615 | 280.125 |
| % Hydrophobic | % Polar |
|---|---|
| 61.45 | 38.55 |
| According to VolSite | |
| HET Code: | MTA |
|---|---|
| Formula: | C11H15N5O3S |
| Molecular weight: | 297.333 g/mol |
| DrugBank ID: | DB02282 |
| Buried Surface Area: | 86.81 % |
| Polar Surface area: | 144.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -42.5986 | 5.1962 | -21.7672 |
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 |
| CS | SD | MET- 11 | 4.31 | 0 | Hydrophobic |
| C4' | SD | MET- 11 | 4.04 | 0 | Hydrophobic |
| C3' | CG2 | ILE- 53 | 3.97 | 0 | Hydrophobic |
| CS | CD1 | ILE- 53 | 3.63 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 79 | 4.24 | 0 | Hydrophobic |
| S5' | CD2 | LEU- 105 | 3.69 | 0 | Hydrophobic |
| CS | CE2 | PHE- 108 | 3.88 | 0 | Hydrophobic |
| C5' | CD1 | PHE- 154 | 3.52 | 0 | Hydrophobic |
| N6 | O | VAL- 155 | 3.07 | 147.31 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 155 | 3.01 | 162.45 | H-Bond (Protein Donor) |
| C2' | CB | GLU- 174 | 4.06 | 0 | Hydrophobic |
| C2' | CG | MET- 175 | 3.57 | 0 | Hydrophobic |
| C3' | SD | MET- 175 | 3.82 | 0 | Hydrophobic |
| S5' | SD | MET- 175 | 3.81 | 0 | Hydrophobic |
| O2' | N | MET- 175 | 2.69 | 142.48 | H-Bond (Protein Donor) |
| O2' | OE1 | GLU- 176 | 2.56 | 137.85 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 176 | 3.35 | 149.66 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 176 | 2.61 | 154.5 | H-Bond (Ligand Donor) |
| N7 | ND2 | ASN- 199 | 2.82 | 173.78 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 199 | 3.02 | 162.51 | H-Bond (Ligand Donor) |
| CS | CZ | PHE- 209 | 3.79 | 0 | Hydrophobic |
| C1' | CE2 | PHE- 209 | 4.46 | 0 | Hydrophobic |
| C4' | CE2 | PHE- 209 | 3.78 | 0 | Hydrophobic |
