sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2010-10-05
| Name: | Adenosine kinase, putative |
|---|---|
| ID: | Q584S0_TRYB2 |
| AC: | Q584S0 |
| Organism: | Trypanosoma brucei brucei |
| Reign: | Eukaryota |
| TaxID: | 185431 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.196 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.104 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 60.69 | 39.31 |
| According to VolSite | |
| HET Code: | KRM |
|---|---|
| Formula: | C19H19N3O2 |
| Molecular weight: | 321.373 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 43.42 % |
| Polar Surface area: | 50.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 18.4125 | -28.5742 | 6.49983 |
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 |
| C23 | SG | CYS- 12 | 4.27 | 0 | Hydrophobic |
| C24 | CB | ASN- 13 | 3.7 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 15 | 4.24 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 39 | 4.49 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 39 | 3.75 | 0 | Hydrophobic |
| C23 | CB | SER- 64 | 3.98 | 0 | Hydrophobic |
| C21 | CB | SER- 64 | 4.31 | 0 | Hydrophobic |
| O22 | N | SER- 64 | 3.14 | 165.41 | H-Bond (Protein Donor) |
| C11 | CD2 | LEU- 138 | 3.95 | 0 | Hydrophobic |
| C21 | CE1 | PHE- 169 | 3.71 | 0 | Hydrophobic |
| C20 | CZ | PHE- 169 | 4.06 | 0 | Hydrophobic |
| C23 | CD1 | PHE- 169 | 3.8 | 0 | Hydrophobic |
| C12 | CG2 | THR- 172 | 3.79 | 0 | Hydrophobic |
| C4 | CB | PHE- 200 | 4.37 | 0 | Hydrophobic |
| N18 | O | HOH- 2017 | 2.77 | 152.52 | H-Bond (Protein Donor) |
