The non-protein component is a very potent DNA-damaging agent; However it is extremely unstable and the role of the protein is to protect it and release it to the target DNA.

[clarification needed] The biosynthesis of neocarzinostatin takes place through a convergence of the activities of a gene cluster, which includes two separate iterative type I polyketide synthase (PKS) and deoxy sugar biosynthetic pathways.

Additionally, a cluster of NcsC genes are responsible for coding enzymes for the synthesis of the deoxyamino sugar moiety of NCS chromophore.

Synthesis of deoxyaminosugar moiety: This part is carried out by the enzymes encoded by a cluster of seven genes, named NcsC through Ncs6.

There is an additional carbonate functionality added, probably originating from CO2 (or bicarbonate), however, it remains to be determined whether this step is truly enzymatic.