sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2012-01-17
| Name: | Putative adenosine kinase |
|---|---|
| ID: | G4V7G8_SCHMA |
| AC: | G4V7G8 |
| Organism: | Schistosoma mansoni |
| Reign: | Eukaryota |
| TaxID: | 6183 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 28.515 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.430 | 553.500 |
| % Hydrophobic | % Polar |
|---|---|
| 40.85 | 59.15 |
| According to VolSite | |
| HET Code: | 2FA |
|---|---|
| Formula: | C10H12FN5O4 |
| Molecular weight: | 285.232 g/mol |
| DrugBank ID: | DB04441 |
| Buried Surface Area: | 75.62 % |
| Polar Surface area: | 139.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 12.9829 | -14.1983 | 8.26635 |
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 |
| N1 | ND2 | ASN- 14 | 3.3 | 160.32 | H-Bond (Protein Donor) |
| F | CD1 | LEU- 16 | 4.12 | 0 | Hydrophobic |
| O2' | OD2 | ASP- 18 | 3.25 | 132.39 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 18 | 2.74 | 151.52 | H-Bond (Ligand Donor) |
| O2' | N | GLY- 64 | 3.26 | 162.24 | H-Bond (Protein Donor) |
| C1' | CB | ALA- 65 | 4.47 | 0 | Hydrophobic |
| F | CB | ALA- 65 | 4.41 | 0 | Hydrophobic |
| N3 | N | ALA- 65 | 3.21 | 165.91 | H-Bond (Protein Donor) |
| O3' | ND2 | ASN- 68 | 2.87 | 133.09 | H-Bond (Protein Donor) |
| C2' | CG2 | VAL- 123 | 4.12 | 0 | Hydrophobic |
| C5' | CE | MET- 134 | 3.86 | 0 | Hydrophobic |
| C2' | SD | MET- 134 | 3.91 | 0 | Hydrophobic |
| N7 | OG1 | THR- 136 | 2.96 | 162.34 | H-Bond (Protein Donor) |
| F | CB | PHE- 169 | 3.63 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 169 | 3.78 | 0 | Aromatic Face/Face |
| O5' | OD2 | ASP- 302 | 2.75 | 153.29 | H-Bond (Ligand Donor) |
| N6 | O | HOH- 517 | 3 | 144.75 | H-Bond (Ligand Donor) |
