Inositol phosphates (InsPs) are signaling molecules with multiple roles in cells. In particular (InsP ₆ ) is involved in mRNA export and editing or chromatin remodeling among other events. InsP ₆ accumulates as mixed salts (phytate) in storage tissues of plants and plays a key role in their physiology. Human diets that are exclusively grain-based provide an excess of InsP ₆ that, through chelation of metal ions, may have a detrimental effect on human health. Ins(1,3,4,5,6)P ₅ 2-kinase (InsP ₅ 2-kinase or Ipk1) catalyses the synthesis of InsP ₆ from InsP ₅ and ATP, and is the only enzyme that transfers a phosphate group to the axial 2-OH of the myo-inositide. We present the first structure for an InsP ₅ 2-kinase in complex with both substrates and products. This enzyme presents a singular structural region for inositide binding that encompasses almost half of the protein. The key residues in substrate binding are identified, with Asp368 being responsible for recognition of the axial 2-OH. This study sheds light on the unique molecular mechanism for the synthesis of the precursor of inositol pyrophosphates.