A novel pharmacophore descriptor Flexophore is presented, which considers molecular flexibility when comparing descriptor similarities. The descriptor is a complete reduced graph of the underlying molecule. Its nodes are represented by enhanced MM2 atom types, while the edge descriptions encode the molecular flexibility by means of a histogram of node distances in a diverse conformer distribution. For comparing two descriptor nodes, a statistical function derived from the Cambridge Crystallographic Database is implemented. To assess the capability of the descriptor to describe the bioactivity space, 350 test data sets with 1000 molecules each are compiled. The data sets were spiked with molecules active on one of 18 different targets. In 175 of the 350 data sets, all molecules chemically similar to the query molecules were removed. Virtual screening on these data sets showed that the Flexophore descriptor detects active molecules despite chemical dissimilarity, whereas the results for the screening of the complete data sets show enrichments comparable to chemical fingerprint descriptors. The diversity analysis of the enriched compounds demonstrates that the Flexophore descriptor describes the chemical space orthogonal to chemical fingerprint descriptors.