Pyrabactin is a synthetic mimicry of abscisic acid (ABA). While ABA and pyrabactin share the same pocket in the PYL/RCARs, pyrabactin modulates ABA signaling differently. Functionality of pyrabactin is known to depend on polymorphism of specific residues in Arabidopsis PYL/RCARs in subfamily-dependent manners. To explore structural determinants for differential effects of pyrabactin in rice PYL/RCARs, we determined the crystal structure of OsPYL/RCAR3:pyrabactin:OsPP2C50. Pyrabactin in rice adopts a conformation unobserved for pyrabactin in Arabidopsis. Phe125, specific to the subfamily I of OsPYL/RCARs in the ABA binding pocket, appears to be the culprit for the differential conformation of pyrabactin. Phe125 apparently restricts accessibility of pyrabactin, leading to decreased affinity for OsPYL/RCAR3, evidenced by phosphatase assay. However, Phe125 does not affect conformation and accessibility of ABA, corroborated by gene transcription analyses. Our results suggest that phenylalanine substitution of OsPYL/RCARs subfamily I may be one of considerations for ABA synthetic agonist development.