sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2007-04-18
| Name: | Adenosine kinase |
|---|---|
| ID: | ADOK_MYCTU |
| AC: | P9WID5 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 2.7.1.20 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.904 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.209 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 70.00 | 30.00 |
| According to VolSite | |
| HET Code: | ACP |
|---|---|
| Formula: | C11H14N5O12P3 |
| Molecular weight: | 501.176 g/mol |
| DrugBank ID: | DB03909 |
| Buried Surface Area: | 52.66 % |
| Polar Surface area: | 310.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 16.6401 | 68.5903 | 6.39435 |
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 |
| O1B | ND2 | ASN- 195 | 3.26 | 163 | H-Bond (Protein Donor) |
| O2A | OG1 | THR- 223 | 3.04 | 136.28 | H-Bond (Protein Donor) |
| O3A | OG1 | THR- 223 | 3.32 | 157.93 | H-Bond (Protein Donor) |
| C5' | CB | THR- 223 | 3.74 | 0 | Hydrophobic |
| O2A | N | GLY- 225 | 2.67 | 143.41 | H-Bond (Protein Donor) |
| O3' | O | GLY- 228 | 2.87 | 145.54 | H-Bond (Ligand Donor) |
| C2' | CG1 | VAL- 243 | 3.8 | 0 | Hydrophobic |
| C4' | CG1 | VAL- 255 | 4.41 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 255 | 3.92 | 0 | Hydrophobic |
| C4' | CB | PHE- 259 | 3.98 | 0 | Hydrophobic |
| C4' | CB | ALA- 284 | 4.37 | 0 | Hydrophobic |
| C1' | CB | ALA- 284 | 3.53 | 0 | Hydrophobic |
