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Cofactor lens / chemistry across pathways

Follow the chemistry that pathways share.

Vitamins are precursors; active cofactors are working molecular forms. This lens connects twelve cofactor systems to the compounds and reactions represented in the current graph, revealing recurring transfer, redox, rearrangement, and catalytic strategies.

Vitamin-to-reaction vocabulary

Twelve reusable chemical strategies

Reaction matches come from controlled cofactor aliases found in release event names, equations, and catalyst annotations. They describe representation in this release, not measured abundance or pathway rate.

Connecting the vocabulary to the graph…

Release human-metabolism-r97-map-v2
Resolving cofactor neighborhoods

Matching controlled cofactor terms within release event records.

carbon transfer / oxidative decarboxylation

TDP · vitamin B1

Thiamin diphosphate is the activated B1 form used to stabilize carbon fragments during oxidative decarboxylation and two-carbon transfer reactions.

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    redox

    FAD/FMN · vitamin B2

    Riboflavin-derived FAD and FMN carry one or two electrons, often while bound within enzymes that couple difficult oxidation and reduction steps.

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      hydride transfer

      NAD/NADP · vitamin B3

      Niacin-derived NAD and NADP carry hydride equivalents. Their phosphorylated and unphosphorylated pools support distinct, though connected, redox economies.

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        acyl transfer

        CoA · vitamin B5

        Pantothenate-derived coenzyme A uses a reactive thiol to form thioesters, activating acyl groups for transfer, oxidation, and biosynthesis.

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          amino-acid chemistry

          PLP · vitamin B6

          Pyridoxal phosphate forms reversible covalent intermediates that stabilize amino-acid reaction chemistry, including transamination, decarboxylation, and elimination.

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            carboxyl transfer

            Biotin · vitamin B7

            Biotin is an enzyme-tethered carbon-dioxide carrier. ATP-dependent carboxylases move its activated carboxyl group between catalytic sites.

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              one-carbon transfer

              THF · vitamin B9

              Reduced folate forms carry one-carbon units at several oxidation states, linking serine and glycine chemistry to nucleotides and methyl-group metabolism.

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                rearrangement / methyl transfer

                Cobalamin · vitamin B12

                Cobalt-containing cobalamin supports radical rearrangement and methyl-transfer chemistry in a small but metabolically consequential set of human enzymes.

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                  electron transfer / oxygen chemistry

                  Heme

                  The iron–porphyrin framework of heme enables electron transfer, oxygen handling, and peroxide chemistry across respiratory and oxidative enzyme systems.

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                    electron transfer / enzyme structure

                    Fe–S clusters

                    Iron–sulfur clusters provide tunable electron-transfer centers and structural catalytic elements assembled and distributed by dedicated cellular machinery.

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                      membrane electron carrier

                      Ubiquinone

                      Ubiquinone is a lipid-soluble electron and proton carrier that moves within membranes, connecting multiple dehydrogenases to respiratory electron transfer.

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                        thiol redox / conjugation

                        Glutathione

                        Glutathione is a cysteine-containing tripeptide used in thiol redox buffering, peroxide reduction, and conjugation reactions.

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                          Reading key

                          Precursor, active form, reaction role.

                          A nutrient label and the exact molecule participating in an enzyme reaction are not always the same. Keep those levels separate as you move through the lens.

                          01

                          Vitamin precursor

                          The dietary or transported family from which an active cofactor can be produced.

                          02

                          Activated molecular form

                          The chemically specific species used, transferred, reduced, oxidized, or enzyme-bound.

                          03

                          Reaction neighborhood

                          The release events whose names, equations, or catalyst annotations match the controlled vocabulary.

                          04

                          Biological context

                          Compartment, enzyme, pathway, and cellular state determine what that chemistry means.