sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2002-04-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.050 | 5.050 | 5.050 | 0.000 | 5.050 | 1 |
| 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: | 23.170 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.780 | 722.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.33 | 54.67 |
| According to VolSite | |
| HET Code: | ADN |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | DB00640 |
| Buried Surface Area: | 54.17 % |
| 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 |
|---|---|---|
| 150.064 | 13.9318 | -5.91058 |
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 | 4.26 | 0 | Hydrophobic |
| C2' | CG2 | VAL- 302 | 3.7 | 0 | Hydrophobic |
| C5' | CB | ALA- 316 | 4.03 | 0 | Hydrophobic |
| O2' | OD1 | ASN- 342 | 3.21 | 146.67 | H-Bond (Ligand Donor) |
| C4' | CB | ALA- 345 | 3.87 | 0 | Hydrophobic |
| C1' | CB | ALA- 345 | 4.15 | 0 | Hydrophobic |
| N3 | NE2 | GLN- 346 | 3.18 | 134.17 | H-Bond (Protein Donor) |
| O3' | O | HOH- 1043 | 3.12 | 155.35 | H-Bond (Ligand Donor) |
