Biological molecules include the compounds made, transformed, or used by living systems. This dataset concentrates on chemically defined small molecules—amino acids, sugars, nucleobases, cofactors, vitamins, lipids, neurotransmitters, and metabolites—rather than whole proteins or long nucleic-acid polymers.
The categories overlap by design. A molecule can be both a metabolite and a signaling compound, or both a vitamin-derived cofactor and part of an enzyme reaction. ChEBI identifiers help connect those roles to a controlled chemical ontology.
From building blocks to macromolecules
Amino acids are the building blocks of proteins, and nucleotides form DNA and RNA. Monosaccharides can be joined into larger carbohydrates, while many lipids assemble into membranes or act as energy stores and signals.
Small metabolites also connect biochemical pathways. ATP transfers chemical energy, NAD-related cofactors carry electrons, and central-carbon metabolites link glycolysis, the citric-acid cycle, amino-acid metabolism, and biosynthesis.
Chemical form matters
Biological pH, stereochemistry, protonation, metal binding, and cellular compartment can change the chemically relevant form of a molecule. A database row is therefore a defined reference structure, not a claim that only one form exists in every biological setting.
How this dataset was assembled
ChEBI is the preferred ontology source for biological roles and chemical classes; PubChem supplies compound identifiers and structures. HMDB is useful for metabolite expansion but needs license review before redistribution.
Each row retains source identifiers where available. Molecular weight is calculated from the recorded formula, and the original names, structures, classifications, and database links remain visible so individual entries can be checked before reuse.
People also ask
What are the four major types of biological molecules?
Carbohydrates, lipids, proteins, and nucleic acids are the four major macromolecular classes. This table mainly contains their small building blocks, cofactors, metabolites, and related signaling molecules.
What is the difference between a metabolite and a biomolecule?
Biomolecule is the broader term. A metabolite is a relatively small compound that participates in metabolism as a reactant, intermediate, or product.
Are vitamins biological molecules?
Yes. Vitamins are organic micronutrients required in small amounts, and many are converted into cofactors or coenzymes that support enzyme reactions.
Why do biological databases use ChEBI IDs?
ChEBI provides stable identifiers plus relationships for chemical classes and biological roles, which makes it easier to connect the same compound across experiments, pathways, and databases.
Sources and further reading
ChEBI — Chemical ontology classes, biological roles, synonyms, formulas, SMILES, InChI, and ChEBI identifiers.
PubChem — Canonical compound identifiers, names, formulas, structures, SMILES, and downloadable compound records.
RDKit — Derived descriptors such as molecular weight, LogP, TPSA, hydrogen-bond counts, and canonicalized structures.