How is protein cavity centre related to binding?
As you can find under the table with cavity centers in pdf version of this article:


  The table lists the protein’s PDB ID, the ligand considered and the specified cavity center. 22 ligands are similar to hexoses in shape and/or size. The cavity center is the centroid of the reported PDB atom numbers.


And a little later:


  The binding-site center is computed as the
  hexose pyranose ring centroid for the positive examples,
  and as the ligand or empty pocket centroid for the negative
  ones. The hexose pyranose-ring atoms are located up to
  2.9
   ̊
  A away from the ring’s centroid. Since some atomic
  interactions can be important up to 7
   ̊
  A [22], we consider
  the binding-site as all protein atoms present within a 10
   ̊
  A radius sphere around the binding center. All other atoms
  are discarded.


So basically @aandreev is right. You can read about centroids here