5-F-IAA contains an indole-3-acetic acid scaffold bearing a fluorine substituent at the 5-position, classifying it as a fluorinated, non-proteinogenic amino acid derivative rather than a standard proteinogenic amino acid. The molecule retains the amino acid functional motif with a carboxylic acid group and a side-chain carbon framework characteristic of indoleacetic acid, while the aromatic indole ring substitution modulates electronic and physicochemical properties relevant to binding and reactivity; stereochemistry is not specified in the product name. 5-F-IAA is used in chemical biology and analytical method development as a fluorinated handle for studying structure-property relationships, supporting isotopic or fluorine-based detection strategies, and serving as a precursor for preparing related indoleacetic acid analogues and conjugatable derivatives for labeling or structure-activity studies.
CAT No: CP25848
CAS No:443-73-2
Synonyms/Alias:5-Fluoroindole-3-aceticacid;443-73-2;2-(5-fluoro-1H-indol-3-yl)aceticacid;(5-fluoro-1H-indol-3-yl)aceticacid;NSC88616;5-Fluoro-1H-indole-3-aceticacid;NSC-88616;SBB066676;1h-indole-3-aceticacid,5-fluoro-;PubChem7277;AC1Q4NE6;NCIStruc1_000046;NCIStruc2_000019;CHEMBL82870;F4506_SIGMA;5-fluoro-indol-3-aceticacid;5-fluoro-indole-3-aceticacid;AC1L3X53;SCHEMBL2260803;5-FLUOROINDOLE-3aceticacid;CTK1D6143;(5-fluoro-3-indolyl)aceticacid;GWLLOJBOPVNWNF-UHFFFAOYSA-N;MolPort-000-155-597;ZINC402910
Chemical Name:5-Fluoroindole-3-acetic acid, 98%
5-F-IAA is a fluorinated indole-containing amino acid derivative commonly used in chemical biology and medicinal chemistry workflows that require a halogenated tryptophan analog for structure-activity studies and labeling strategies. Its aromatic indole framework and fluorine substitution provide a distinct electronic and steric signature that can be leveraged in receptor-binding and binding-mode investigations, as well as in isotope-free analytical differentiation by mass spectrometry. As a small-molecule amino acid building block, 5-F-IAA is typically handled as a research reagent for incorporation into synthetic constructs, affinity reagents, or assay-ready standards where the fluorine substituent serves as a chemically informative tag.
1. Peptidomimetic Building Blocks
5-F-IAA is used as an amino acid building block for preparing peptidomimetics and indole-based analogs in medicinal chemistry programs, where the fluorinated indole motif helps probe how aromatic electronics influence binding and downstream structure-activity relationships. Researchers in small-molecule and peptide-drug discovery often select 5-F-IAA to introduce a defined fluorine substituent into a larger scaffold, enabling clean comparative studies against non-fluorinated analogs. In downstream workflows, the compound supports the synthesis of constrained or functionalized analog series that are evaluated in biochemical binding assays, SAR mapping, and lead-optimization iterations.
2. Chemical Biology Binding Studies
5-F-IAA is frequently employed in chemical biology experiments designed to interrogate indole-binding interactions, including receptor- and protein-ligand systems where indole recognition is a key determinant. The fluorine substitution provides a chemically distinct handle for orthogonal analytical readouts, supporting workflows that rely on LC-MS confirmation of compound identity and purity across screening and follow-up experiments. Chemical biology groups use 5-F-IAA to generate probe-like analogs, competitive ligands, or assay standards that help clarify binding specificity trends within a defined experimental series.
3. Analytical Standards And MS Tracing
5-F-IAA is used as an analytical reference compound for method development and validation in LC-MS workflows that require fluorinated indole standards with a predictable mass signature. Analytical chemists and metabolomics-oriented groups often incorporate 5-F-IAA into calibration/qualification sets to verify retention behavior, ionization response, and identification criteria for fluorinated aromatic species. Because the fluorine substituent creates a distinct fragmentation and mass shift relative to non-fluorinated analogs, 5-F-IAA is also applied as a stable, non-isotopic comparator for confirming the presence of fluorinated targets or intermediates in complex mixtures.
4. Reagent For Probe Derivatization
5-F-IAA serves as a starting building block for derivatization toward indole-based chemical probes used in target engagement and interaction-mapping studies. In practice, researchers attach 5-F-IAA-derived motifs to larger probe scaffolds to create assay-ready reagents that preserve the fluorinated indole recognition element while adding functionality for downstream detection or immobilization. This application is particularly common in labs developing ligand-based probes for binding confirmation, pull-down workflows, or surface/solid-phase assays where a chemically stable aromatic tag is required to track probe behavior through purification and analytical characterization.
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