Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the chemical structure for a given compound is not necessarily consistent between databases. This paper presents StructRecon, a novel tool for resolving unique and correct molecular structures from database identifiers. StructRecon traverses the cross-links between database entries in different databases to construct what we call an identifier graph, which offers a more complete view of the total information available on a particular compound across all the databases. In order to reconcile discrepancies between databases, we first present an extensible model for chemical structure which supports multiple independent levels of detail, allowing standardisation of the structure to be applied iteratively. In some cases, our standardisation approach results in multiple structures for a given compound, in which case a random walk-based algorithm is used to select the most likely structure among incompatible alternates. We applied StructRecon to the EColiCore2 model, resolving a unique chemical structure for 85.11 % of identifiers. StructRecon is open-source and modular, which enables the potential support for more databases in the future.