his dataset contains immunoprecipitation coupled with mass spectrometry (IP-MS) data for identifying candidate interacting proteins of PCD11 (LOC_Os11g41710), a cytochrome P450 protein negatively regulating grain number per panicle in rice. PCD11-GFP was immunoprecipitated from 1 cm young panicles using anti-GFP antibody, with normal mouse IgG as control. LC-MS/MS was performed on a Thermo Orbitrap Astral. A total of 788 differentially enriched proteins were identified (|log2FC| > 0.585), including hormone signaling components (OsBSK3, PP2A, BIG) and membrane trafficking proteins, providing clues to PCD11's regulatory mechanism.