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An amidine is a nitrogen analogue of an oxoacid derivative. In ordinary organic-chemistry usage it most often means a carboxamidine, whose central carbon is bonded to two nitrogens, conventionally represented by $\mathrm{R}-\mathrm{C}(=\mathrm{N}{\mathrm{R}}_1)-\mathrm{N}({\mathrm{R}}_2){\mathrm{R}}_3$. The IUPAC class is broader than only carbon-centred examples, so the intended structural subclass should be stated.^[ref]

A simple unsubstituted-nitrogen pattern is $\mathrm{R}-\mathrm{C}(=\mathrm{NH})-\mathrm{N}{\mathrm{H}}_2$. Choosing $\mathrm{R}=\mathrm{C}{\mathrm{H}}_3$ gives $\mathrm{C}{\mathrm{H}}_3-\mathrm{C}(=\mathrm{NH})-\mathrm{N}{\mathrm{H}}_2$ and an atom count of ${\mathrm{C}}_2{\mathrm{H}}_6{\mathrm{N}}_2$. Compare an amide, $\mathrm{R}-\mathrm{C}(=\mathrm{O})-\mathrm{N}{\mathrm{H}}_2$: replacing the doubly bonded oxygen with an imino nitrogen changes the characteristic group. Similar spelling does not make the two classes chemically identical.

Imidoesters react with amines to give amidines. This conversion connects a functional-group definition with experimental protein cross-linking, where amino groups on a protein can be modified by an appropriate reagent.^[ref] The structural pattern alone does not specify one reaction rate or one acid–base constant for every substituted amidine.

An imidoester is an ester of an imidic acid. A common carbon-centred pattern is $\mathrm{R}-\mathrm{C}(=\mathrm{NH})-\mathrm{O}{\mathrm{R}}^{\prime }$, with an imino nitrogen in place of the carbonyl oxygen of an ordinary ester. Imidoesters react with amines to form amidines, which makes them useful for modifying protein amino groups.^[ref]

A formal net substitution illustrates the group change:The product has a carbon bonded to two nitrogens rather than an alkoxy group. This equation is structural bookkeeping, not a claim about every protonation state, kinetic pathway or experimental yield.

A bifunctional reagent such as dimethyl suberimidate has two reactive ends and can connect two amino groups. Those groups can lie on different proteins or within one folded protein.^[ref] Thus a detected cross-link constrains which reactive sites could be connected under the assay conditions; it is not automatically proof of direct atom-to-atom contact or a unique unperturbed protein arrangement.