The nomenclature for this biomolecule can be confusing: Molybdopterin itself contains no molybdenum; rather, this is the name of the ligand (a pterin) that will bind the active metal.

Molybdopterin consists of a pyranopterin, a complex heterocycle featuring a pyran fused to a pterin ring.

In addition, the pyran ring features two thiolates, which serve as ligands in molybdo- and tungstoenzymes.

Molybdenum cofactor biosynthesis occurs in four steps: (i) the radical-mediated cyclization of nucleotide, guanosine triphosphate (GTP), to (8S)‑3',8‐cyclo‑7,8‑dihydroguanosine 5'‑triphosphate (3',8‑cH2GTP), (ii) the formation of cyclic pyranopterin monophosphate (cPMP) from the 3',8‑cH2GTP, (iii) the conversion of cPMP into molybdopterin (MPT), (iv) the insertion of molybdate into MPT to form Moco.

The monophosphate is adenylated (coupled to ADP) in a step that activates the cofactor toward binding Mo or W. These metals are imported as their oxyanions, molybdate, and tungstate.