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The stabilization of G-quadruplex DNA structures by small molecules with affinity to oncogene promoters has emerged as a promising anticancer strategy, due to a potential role in gene expression regulation. We explored the ability of BMH-21 (<b>1</b>) and its analogue BA-41 (<b>2</b>) to bind the G-quadruplex structure present in the c-KIT promoter by biophysical methods and molecular modeling. We provide evidence that both compounds interact with the c-KIT 21-mer sequence. The stable monomeric intramolecular parallel G-quadruplex obtained by the mutation of positions 12 and 21 allowed the precise determination of the binding mode by NMR and molecular dynamics studies. Both compounds form a complex characterized by one ligand molecule positioned over the tetrad at the 3&#8242;-end, stabilized by an extensive network of &#960;&#8722;&#960; interactions. The binding constants (Kb) obtained with fluorescence are similar for both complexes (around 10⁶ M^&#8722;1). Compound BA-41 (<b>2</b>) showed significant antiproliferative activity against a human lymphoma cell line, SU-DHL4, known to express substantial levels of c-KIT. However, the partial inhibition of c-KIT expression by Western blot analysis suggested that the interaction of compound <b>2</b> with the c-KIT promoter is not the primary event and that multiple effects provide a contribution as determinants of biological activity.