To discover new catalysts using density functional theory (DFT) calculations, binding energies of reaction intermediates are considered as descriptors to predict catalytic activities. Recently, machine learning methods have been developed to reduce the number of computationally intensive DFT calculations for a high-throughput screening. These methods require several steps such as bulk structure optimization, surface structure modeling, and active site identification, which could be time-consuming as the number of new candidate materials increases. To bypass these processes, in this work, we report an atomic structure-free representation of active motifs to predict binding energies. We identify binding site atoms and their nearest neighboring atoms positioned in the same layer and the sublayer, and their atomic properties are collected to construct fingerprints. Our method enabled a quicker training (200-400 s using CPU) compared to the previous deep-learning models and predicted CO and H binding energies with mean absolute errors (MAEs) of 0.120 and 0.105 eV, respectively. Our method is also capable of creating all possible active motifs without any DFT calculations and predicting their binding energies using the trained model. The predicted binding energy distributions can suggest promising candidates to accelerate catalyst discovery.