sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2005-07-13
| Name: | Adenosine kinase |
|---|---|
| ID: | ADK_TOXGO |
| AC: | Q9TVW2 |
| Organism: | Toxoplasma gondii |
| Reign: | Eukaryota |
| TaxID: | 5811 |
| EC Number: | 2.7.1.20 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.986 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.903 | 654.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.24 | 58.76 |
| According to VolSite | |
| HET Code: | MTP |
|---|---|
| Formula: | C11H14N4O4S |
| Molecular weight: | 298.318 g/mol |
| DrugBank ID: | DB02896 |
| Buried Surface Area: | 54.99 % |
| Polar Surface area: | 138.82 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 |
|---|---|---|
| -25.9387 | -49.6073 | -111.699 |
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 |
| C5' | CB | THR- 278 | 3.84 | 0 | Hydrophobic |
| C3' | CB | THR- 278 | 4.41 | 0 | Hydrophobic |
| CS | CB | HIS- 281 | 3.73 | 0 | Hydrophobic |
| C2' | CG1 | VAL- 302 | 3.82 | 0 | Hydrophobic |
| CS | CG1 | VAL- 305 | 4.12 | 0 | Hydrophobic |
| O5' | O | ALA- 316 | 3.01 | 120.77 | H-Bond (Ligand Donor) |
| C5' | CB | ALA- 316 | 4.33 | 0 | Hydrophobic |
| C5' | CB | PHE- 320 | 4.43 | 0 | Hydrophobic |
| C4' | CD1 | PHE- 320 | 4.45 | 0 | Hydrophobic |
| O2' | OD1 | ASN- 342 | 2.68 | 140.01 | H-Bond (Ligand Donor) |
| C4' | CB | ALA- 345 | 3.7 | 0 | Hydrophobic |
| C1' | CB | ALA- 345 | 3.71 | 0 | Hydrophobic |
| N3 | NE2 | GLN- 346 | 3.12 | 140.58 | H-Bond (Protein Donor) |
| O3' | O | HOH- 3074 | 2.99 | 162.05 | H-Bond (Ligand Donor) |
