sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2013-12-15
| 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: | 22.648 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.014 | 313.875 |
| % Hydrophobic | % Polar |
|---|---|
| 62.37 | 37.63 |
| According to VolSite | |
| HET Code: | AGS |
|---|---|
| Formula: | C10H14N5O12P3S |
| Molecular weight: | 521.231 g/mol |
| DrugBank ID: | DB02930 |
| Buried Surface Area: | 57.74 % |
| Polar Surface area: | 329.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -4.211 | 6.81826 | -17.7447 |
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 | 2.91 | 164.65 | H-Bond (Protein Donor) |
| O2A | OG1 | THR- 223 | 2.72 | 156.76 | H-Bond (Protein Donor) |
| C3' | CB | THR- 223 | 4.15 | 0 | Hydrophobic |
| C5' | CB | THR- 223 | 3.71 | 0 | Hydrophobic |
| O2A | N | GLY- 225 | 2.96 | 142.53 | H-Bond (Protein Donor) |
| O3' | O | GLY- 228 | 2.72 | 153.46 | H-Bond (Ligand Donor) |
| C2' | CG1 | VAL- 243 | 3.63 | 0 | Hydrophobic |
| N6 | OE2 | GLU- 246 | 3.44 | 144.71 | H-Bond (Ligand Donor) |
| C1' | CG1 | VAL- 255 | 4.14 | 0 | Hydrophobic |
| C5' | CG1 | VAL- 255 | 3.93 | 0 | Hydrophobic |
| O2G | N | GLY- 256 | 2.78 | 153.18 | H-Bond (Protein Donor) |
| C4' | CB | PHE- 259 | 4.25 | 0 | Hydrophobic |
| C4' | CB | ALA- 284 | 4.2 | 0 | Hydrophobic |
| C1' | CB | ALA- 284 | 3.71 | 0 | Hydrophobic |
