How to enter experimental data

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Most information on how to enter experimental data is available through the help icons (question marks) on the submit page. Here additional information is supplied.

General information

Submission of an observation works as a two-step procedure

1. Enter substrate and product structures and meta-data describing the experiment

2. Select atom mappings for the reaction

When editing or curating an observation all things can be done in a single step.

Atom mapping

Atom mapping of enzymatic reactions is included to enable more accurate site-of-metabolism models to be built in the future. All atom mappings used in XMetDB should be labelled certain/uncertain, where certain means that as far as possible we know at which atom (or atoms) the reaction is initiated (for some biotransformations it is impossible to determine to atomic accuracy at which position the reaction starts, e.g. epoxidation which can start at either of the two carbons in the double bond, in which case we select both atoms and label them certain). In the product, newly introduced atoms by the metabolism should be selected (except for conjugation reactions, in which case only the atom connecting the substrate and the conjugate needs to be selected, see for example GST below).

Below follows a list of the common enzyme families, and how proper atom mapping is performed for the common reaction mechanisms performed by these enzymes.

Cytochromes P450

Alcohol oxidation

Reaction Substrate Product
P450-alcoholoxidation.png P450-alcoholoxidation substrate.png P450-alcoholoxidation product.png

Aldehyde oxidation

Reaction Substrate Product
P450-aldehydeoxidation.png P450-aldehydeoxidation substrate.png P450-aldehydeoxidation product.png

Aldehyde deformylation

Reaction Substrate Product
P450-aldehydedeformylation.png P450-aldehydedeformylation substrate.png P450-aldehydedeformylation product.png

Hydroxylation of aliphatic sp3 hybridized carbon atoms

Reaction Substrate Product
P450-aliphatichydroxylation.png P450-aliphatichydroxylation substrate.png P450-aliphatichydroxylation product.png

N-dealkylation

Reaction Substrate Product
P450-ndealkylation.png P450-ndealkylation substrate.png P450-ndealkylation product.png

O-dealkylation

Reaction Substrate Product
P450-odealkylation.png P450-odealkylation substrate.png P450-odealkylation product.png

Epoxidation of alkenes

Reaction Substrate Product
Alkeneepoxidation.png P450-alkeneepoxidation substrate.png P450-alkeneepoxidation product.png

Hydroxylation of aromatic carbons

Reaction Substrate Product
P450-aromatichydroxylation.png P450-aromatic substrate.png P450-aromatichydroxylation product.png

Epoxidation of aromatic carbons

Reaction Substrate Product
P450-aromaticepoxidation.png P450-aromaticepoxidation substrate.png P450-aromaticepoxidation product.png

Oxidation of aromatic carbons into ketones

Reaction Substrate Product
P450-aromaticketoneoxidation.png P450-aromaticketoneoxidation substrate.png P450-aromaticketoneoxidation product.png

Hydroxylation of aromatic carbons coupled with halogen migration

Reaction Substrate Product
P450-aromatichalogenmigration.png P450-aromatichalogenmigration substrate.png P450-aromatichalogenmigration product.png

N-oxidations

Reaction Substrate Product
P450-noxidation.png P450-noxidation substrate.png P450-noxidation product.png
P450-noxidation2.png P450-noxidation2 substrate.png P450-noxidation2 product.png
P450-noxidation3.png P450-noxidation3 substrate.png P450-noxidation3 product.png

S-oxidations

Reaction Substrate Product
P450-soxidation.png P450-soxidation substrate.png P450-soxidation product.png
P450-soxidation2.png P450-soxidation2 substrate.png P450-soxidation2 product.png
P450-soxidation3.png P450-soxidation3 substrate.png P450-soxidation3 product.png
P450-soxidation4.png P450-soxidation4 substrate.png P450-soxidation4 product.png

Thioester bond splitting

Reaction Substrate Product
P450-thioesther.png P450-thioesther substrate.png P450-thioesther product.png

Desulphurization of phosphorothioates

Reaction Substrate Product
P450-desulfurization.png P450-desulfurization substrate.png P450-desulfurization product.png

Deboronation of boronic acids

Reaction Substrate Product
P450-deboronation.png P450-deboronation substrate.png P450-deboronation product.png

Para and ortho quinone and quinone-imine formations

Reaction Substrate Product
P450-paraquinone.png P450-paraquinone substrate.png P450-paraquinone product.png
P450-orthoquinone.png P450-orthoquinone substrate.png P450-orthoquinone product.png
P450-quinoneimine.png P450-quinoneimine substrate.png P450-quinoneimine product.png

Some ortho quinones can also be formed "spontaneously" after an initial O-dealkylation of an aromatic ring with a hydroxy group ortho to the alkoxy group being O-dealkylated. This is in principle two consecutive reactions, and should be entered as two separate observations. An example of such a reaction is shown below P450-spontorthoquinone.png

Aromatization of partly saturated ring systems

Reaction Substrate Product
P450-dihydropyridine.png P450-dihydropyridine substrate.png P450-dihydropyridine product.png
P450-nringaromatization.png P450-nringaromatization substrate.png P450-nringaromatization product.png

In the bottom reaction above, which carbon is attacked is often hard to determine. However, sometimes a certain atom mapping can be performed on the basis of different metabolites found.

Lyase reaction mechanism

Reaction Substrate Product
P450-lyase.png P450-lyase substrate.png P450-lyase product.PNG

This is a likely atom mapping based on the reaction mechanism suggested by Auchus and Miller

Aldehyde Oxidases

Aldehyde oxidation mechanism

Reaction Substrate Product
Aox-aldehyde.png Aox-aldehyde substrate.png Aox-aldehyde product.png

Imine oxidation mechanism

Reaction Substrate Product
Aox-imine.png Aox-imine substrate.png Aox-imine product.png

Iminium ion oxidation

Reaction Substrate Product
Aox-iminium.png Aox-iminium substrate.png Aox-iminium product.png

Aromatic oxidation of heterocycles

Reaction Substrate Product
Aox-aromatic.png Aox-aromatic substrate.png Aox-aromatic product.png

Reduction of N/S-oxides

Reaction Substrate Product
Aox-reduction.png Aox-reduction substrate.png Aox-reduction product.png

This is an uncertain atom mapping as the actual mechanism for the reaction is not known with atomic detail.

Nitro group reduction

This mechanism occurs in two steps, and the intermediate can be identified in some cases, and should be entered as two observations. The full mechanism is shown here, and below the two observations to enter.

Aox-nitro.png

Reaction Substrate Product
Aox-nitro1.png Aox-nitro1 substrate.png Aox-nitro1 product.png
Aox-nitro2.png Aox-nitro2 substrate.png Aox-nitro2 product.png

These are uncertain atom mappings, as the actual mechanism for the reaction is not known with atomic detail.

Flavin-containing Monooxygenases

Heteroatom oxidation

Both N- and S-oxidations in FMO's are performed through an attack on the heteratom.

Reaction Substrate Product
Fmo-amine.png Fmo-amine substrate.png Fmo-amine product.png
Fmo-sox.png Fmo-sox substrate.png Fmo-sox product.png

Hydroxylamine oxidation

The oxidation of hydroxylamines formed from secondary amines can lead to multiple different products, and usually the nitrone formed is not stable and spontaneously dealkylates. Read the review by Ziegler for more details. An example of a reaction from dimethylamine is shown below. Fmo-hydroxylamine.png

Reaction Substrate Product
Fmo-hydroxylamine2.png Fmo-hydroxylamine substrate.png Fmo-hydroxylamine product.png

Hydrazine oxidation

The oxidation of hydrazines is an N-oxidation followed by spontaneous water elimination and a rearrangement and can be described by the mechanism shown below. See the review by Ziegler for more details and possible secondary products formed from the hydrazone product. Fmo-hydrazine.png

Reaction Substrate Product
Fmo-hydrazine2.png Fmo-hydrazine substrate.png Fmo-hydrazine product.png

Monoamine oxidases

Deamination

Mao-deamination.png

Reaction Substrate Product
Mao-deamination2.png Mao-deamination substrate.png Mao-deamination product.png

Alcohol dehydrogenases

Alcohol dehydrogenation

Reaction Substrate Product
Adh-alcohol.png Adh-alcohol substrate.png Adh-alcohol product.png

Epoxide hydrolases

Diol formation

Reaction Substrate Product
Eph-diol.png Eph-diol substrate.png Eph-diol product.png

Glutathione S-transferases

Conjugation

Reaction Substrate Product
Gst-conjugation.png Gst-conjugation substrate.png Gst-conjugation product.png

Conjugation and dehalogenation

Reaction Substrate Product
Gst-dehalo.png Gst-dehalo substrate.png Gst-dehalo product.png

Sulfotransferases

Sulfotransferases perform a conjugation of sulfuric acid to hydroxyl and amine groups. The mechanism is the same in both cases with an attack on the heteroatom.

Sulfuric acid conjugation

Reaction Substrate Product
Sult-conjugation.png Sult-conjugation substrate.png Sult-conjugation product.png

UDP-glucuronosyltransferases

The glucoronosyltransferases can attach a glucoronic acid to hydroxyl and carboxylic acid groups as shown below.

Glucuronidation of alcohols and carboxylic acids

Reaction Substrate Product
Ugt-alcohol.png Ugt-alcohol substrate.png Ugt-alcohol product.png
Ugt-acid.png Ugt-acid substrate.png Ugt-acid product.png