As the size of accessible compound libraries expands to over 10 billion, the need for more efficient structure-based virtual screening methods is emerging. Different pre-screening methods have been developed to rapidly screen the library, but the structure-based methods applicable to general proteins are still lacking: the challenge is to predict the binding pose between proteins and ligands and perform scoring in an extremely short time. We introduce PharmacoNet, a deep learning framework that identifies the optimal 3D pharmacophore arrangement which a ligand should have for stable binding from the binding site. By coarse-grained graph matching between ligands and the generated pharmacophore arrangement, we solve the expensive binding pose sampling and scoring procedures of existing methods in a single step. PharmacoNet is significantly faster than state-of-the-art structure-based approaches, yet reasonably accurate with a simple scoring function. Furthermore, we show the promising result that PharmacoNet effectively retains hit candidates even under the high pre-screening filtration rates. Overall, our study uncovers the hitherto untapped potential of a pharmacophore modeling approach in deep learning-based drug discovery.