Molecular Property Diagnostic Suite-Compound Library (MPDS-CL), is an open-source galaxy-based cheminformatics web-portal which presents a structure-based classification of the molecules. A structure-based classification of nearly 150 million unique compounds, which are obtained from 42 publicly available databases were curated for redundancy removal through 97 hierarchically well-defined atom composition-based portions. These are further subjected to 56-bit fingerprint-based classification algorithm which led to a formation of 56 structurally well-defined classes. The classes thus obtained were further divided into clusters based on their molecular weight. Thus, the entire set of molecules was put in 56 different classes and 625 clusters. This led to the assignment of a unique ID, named as MPDS AadharID, for each of these 149 169 443 molecules. MPDS AadharID is akin to the unique number given to citizens in India (similar to the SSN in US, NINO in UK). MPDS-CL unique features are: a) several search options, such as exact structure search, substructure search, property-based search, fingerprint-based search, using SMILES, InChIKey and key-in; b) automatic generation of information for the processing for MPDS and other galaxy tools; c) providing the class and cluster of a molecule which makes it easier and fast to search for similar molecules and d) information related to the presence of the molecules in multiple databases. The MPDS-CL can be accessed at http://mpds.neist.res.in:8086/.