sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2005-07-12
| 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: | 15.551 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.882 | 405.000 |
| % Hydrophobic | % Polar |
|---|---|
| 60.83 | 39.17 |
| According to VolSite | |
| HET Code: | 26A |
|---|---|
| Formula: | C12H17N5O4 |
| Molecular weight: | 295.294 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.72 % |
| Polar Surface area: | 116.76 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 |
|---|---|---|
| -10.2815 | -42.9395 | -104.714 |
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- 20 | 3.14 | 173.07 | H-Bond (Protein Donor) |
| O2' | OD1 | ASP- 24 | 2.68 | 168.75 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 24 | 2.67 | 168.12 | H-Bond (Ligand Donor) |
| C9 | CD2 | LEU- 46 | 3.81 | 0 | Hydrophobic |
| O2' | N | GLY- 69 | 2.97 | 154.05 | H-Bond (Protein Donor) |
| O3' | N | GLY- 69 | 3.3 | 131.81 | H-Bond (Protein Donor) |
| N3 | N | SER- 70 | 3.11 | 156.31 | H-Bond (Protein Donor) |
| O3' | ND2 | ASN- 73 | 3.15 | 153.58 | H-Bond (Protein Donor) |
| C2' | SG | CYS- 127 | 4.08 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 142 | 3.67 | 0 | Hydrophobic |
| C10 | CD2 | TYR- 169 | 3.5 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 169 | 3.8 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 169 | 3.86 | 0 | Aromatic Face/Face |
| C10 | CG2 | THR- 172 | 4.41 | 0 | Hydrophobic |
| O5' | OD2 | ASP- 318 | 2.77 | 173.29 | H-Bond (Ligand Donor) |
| C3' | CE1 | PHE- 354 | 3.76 | 0 | Hydrophobic |
| O5' | O | HOH- 5186 | 2.68 | 146.14 | H-Bond (Protein Donor) |
