List of biological molecules

A curated list of small biological molecules, metabolites, cofactors, amino acids, nucleobases, lipids, and related structures.

Rows
184
Last updated
Version
2026.10.05
License
CC BY 4.0
Formats
CSV, JSON
Sources
ChEBI, PubChem, RDKit
Citation
CSVJSON
WaterH2O18.02Solvent of lifeO962CHEBI:15377
GlycineC2H5NO275.07Amino acidC(C(=O)O)N750CHEBI:15428
L-AlanineC3H7NO289.09Amino acidC[C@@H](C(=O)O)N5950CHEBI:16977
L-ValineC5H11NO2117.15Amino acidCC(C)[C@@H](C(=O)O)N6287CHEBI:16414
L-LeucineC6H13NO2131.18Amino acidCC(C)C[C@@H](C(=O)O)N6106CHEBI:15603
L-IsoleucineC6H13NO2131.18Amino acidCC[C@H](C)[C@@H](C(=O)O)N6306CHEBI:17191
L-ProlineC5H9NO2115.13Amino acidC1C[C@H](NC1)C(=O)O145742CHEBI:17203
L-PhenylalanineC9H11NO2165.19Amino acidC1=CC=C(C=C1)C[C@@H](C(=O)O)N6140CHEBI:17295
L-TryptophanC11H12N2O2204.23Amino acidC1=CC=C2C(=C1)C(=CN2)C[C@@H](C(=O)O)N6305CHEBI:16828
L-TyrosineC9H11NO3181.19Amino acidC1=CC(=CC=C1C[C@@H](C(=O)O)N)O6057CHEBI:17895
L-SerineC3H7NO3105.09Amino acidC([C@@H](C(=O)O)N)O5951CHEBI:17115
L-ThreonineC4H9NO3119.12Amino acidC[C@H]([C@@H](C(=O)O)N)O6288CHEBI:16857
L-CysteineC3H7NO2S121.15Amino acidC([C@@H](C(=O)O)N)S5862CHEBI:17561
L-MethionineC5H11NO2S149.21Amino acidCSCC[C@@H](C(=O)O)N6137CHEBI:16643
L-AsparagineC4H8N2O3132.12Amino acidC([C@@H](C(=O)O)N)C(=O)N6267CHEBI:17196
L-GlutamineC5H10N2O3146.15Amino acidC(CC(=O)N)[C@@H](C(=O)O)N5961CHEBI:18050
L-Aspartic acidC4H7NO4133.10Amino acidC([C@@H](C(=O)O)N)C(=O)O5960CHEBI:17053
L-Glutamic acidC5H9NO4147.13Amino acidC(CC(=O)O)[C@@H](C(=O)O)N33032CHEBI:16015
L-LysineC6H14N2O2146.19Amino acidC(CCN)C[C@@H](C(=O)O)N5962CHEBI:18019
L-ArginineC6H14N4O2174.20Amino acidC(C[C@@H](C(=O)O)N)CN=C(N)N6322CHEBI:16467
L-HistidineC6H9N3O2155.16Amino acidC1=C(NC=N1)C[C@@H](C(=O)O)N6274CHEBI:15971
L-OrnithineC5H12N2O2132.16Non-proteinogenic amino acidC(C[C@@H](C(=O)O)N)CN6262CHEBI:15729
L-CitrullineC6H13N3O3175.19Non-proteinogenic amino acidC(C[C@@H](C(=O)O)N)CNC(=O)N9750CHEBI:16349
L-HomocysteineC4H9NO2S135.18Non-proteinogenic amino acidC(CS)[C@@H](C(=O)O)N91552CHEBI:17588
Beta-alanineC3H7NO289.09Non-proteinogenic amino acidC(CN)C(=O)O239CHEBI:16958
TaurineC2H7NO3S125.14Amino sulfonic acidC(CS(=O)(=O)O)N1123CHEBI:15891
GlutathioneC10H17N3O6S307.32PeptideC(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N124886CHEBI:16856
CarnosineC9H14N4O3226.24PeptideC1=C(NC=N1)C[C@@H](C(=O)O)NC(=O)CCN439224CHEBI:15727
AnserineC10H16N4O3240.26PeptideCN1C=NC=C1C[C@@H](C(=O)O)NC(=O)CCN112072CHEBI:18323
AdenineC5H5N5135.13NucleobaseC1=NC2=NC=NC(=C2N1)N190CHEBI:16708
GuanineC5H5N5O151.13NucleobaseC1=NC2=C(N1)C(=O)NC(=N2)N135398634CHEBI:16235
CytosineC4H5N3O111.10NucleobaseC1=C(NC(=O)N=C1)N597CHEBI:16040
ThymineC5H6N2O2126.12NucleobaseCC1=CNC(=O)NC1=O1135CHEBI:17821
UracilC4H4N2O2112.09NucleobaseC1=CNC(=O)NC1=O1174CHEBI:17568
AdenosineC10H13N5O4267.25NucleosideC1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N60961CHEBI:16335
GuanosineC10H13N5O5283.24NucleosideC1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N135398635CHEBI:16750
CytidineC9H13N3O5243.22NucleosideC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O6175CHEBI:17562
UridineC9H12N2O6244.20NucleosideC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O6029CHEBI:16704
InosineC10H12N4O5268.23NucleosideC1=NC2=C(C(=O)N1)N=CN2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O135398641CHEBI:17596
XanthosineC10H12N4O6284.23NucleosideC1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)NC(=O)NC2=O64959CHEBI:18107
DeoxyadenosineC10H13N5O3251.25NucleosideC1[C@@H]([C@H](O[C@H]1N2C=NC3=C(N=CN=C32)N)CO)O13730CHEBI:17256
DeoxyguanosineC10H13N5O4267.25NucleosideC1[C@@H]([C@H](O[C@H]1N2C=NC3=C2N=C(NC3=O)N)CO)O135398592CHEBI:17172
DeoxycytidineC9H13N3O4227.22NucleosideC1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO)O13711CHEBI:15698
ThymidineC10H14N2O5242.23NucleosideCC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O5789CHEBI:17748
Adenosine triphosphateC10H16N5O13P3507.18NucleotideC1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N5957CHEBI:15422
Adenosine diphosphateC10H15N5O10P2427.20NucleotideC1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O)N6022CHEBI:16761
Adenosine monophosphateC10H14N5O7P347.22NucleotideC1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N6083CHEBI:16027
Guanosine monophosphateC10H14N5O8P363.22NucleotideC1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N135398631CHEBI:17345
Cytidine monophosphateC9H14N3O8P323.20NucleotideC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O6131CHEBI:17361
Uridine monophosphateC9H13N2O9P324.18NucleotideC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O6030CHEBI:16695
Deoxyadenosine monophosphateC10H14N5O6P331.23NucleotideC1[C@@H]([C@H](O[C@H]1N2C=NC3=C(N=CN=C32)N)COP(=O)(O)O)O12599CHEBI:17713
Deoxyguanosine monophosphateC10H14N5O7P347.22NucleotideC1[C@@H]([C@H](O[C@H]1N2C=NC3=C2N=C(NC3=O)N)COP(=O)(O)O)O135398597CHEBI:16192
Thymidine monophosphateC10H15N2O8P322.21NucleotideCC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O9700CHEBI:17013
Orotidine monophosphateC10H13N2O11P368.19NucleotideC1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C(=O)O160617CHEBI:15842
Nicotinamide mononucleotideC11H15N2O8P334.22NucleotideC1=CC(=C[N+](=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)[O-])O)O)C(=O)N14180CHEBI:16171
Nicotinamide adenine dinucleotide (NAD+)C21H27N7O14P2663.43CofactorC1=CC(=C[N+](=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)([O-])OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=NC5=C(N=CN=C54)N)O)O)O)O)C(=O)N5892CHEBI:44215
NADHC21H29N7O14P2665.45CofactorC1C=CN(C=C1C(=O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=NC5=C(N=CN=C54)N)O)O)O)O439153CHEBI:16908
NADP+C21H28N7O17P3743.41CofactorC1=CC(=C[N+](=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)([O-])OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=NC5=C(N=CN=C54)N)OP(=O)(O)O)O)O)O)C(=O)N5885CHEBI:44409
NADPHC21H30N7O17P3745.43CofactorC1C=CN(C=C1C(=O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=NC5=C(N=CN=C54)N)OP(=O)(O)O)O)O)O5884CHEBI:16474
Flavin adenine dinucleotideC27H33N9O15P2785.56CofactorCC1=CC2=C(C=C1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=NC6=C(N=CN=C65)N)O)O)O)O)O643975CHEBI:16238
Flavin mononucleotideC17H21N4O9P456.35CofactorCC1=CC2=C(C=C1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O643976CHEBI:17621
Coenzyme AC21H36N7O16P3S767.53CofactorCC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O87642CHEBI:15346
Acetyl-CoAC23H38N7O17P3S809.57CofactorCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)OP(=O)(O)O)O444493CHEBI:15351
S-AdenosylmethionineC15H22N6O5S398.44CofactorC[S+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)O34755CHEBI:67040
S-AdenosylhomocysteineC14H20N6O5S384.41MetaboliteC1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N439155CHEBI:16680
Lipoic acidC8H14O2S2206.32CofactorC1CSS[C@@H]1CCCCC(=O)O6112CHEBI:30314
HemeC34H32FeN4O4616.50CofactorCC1=C(C2=CC3=C(C(=C([N-]3)C=C4C(=C(C(=N4)C=C5C(=C(C(=N5)C=C1[N-]2)C)C=C)C)C=C)C)CCC(=O)O)CCC(=O)O.[Fe+2]26945-
D-GlucoseC6H12O6180.16MonosaccharideC([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O5793CHEBI:4167
D-FructoseC6H12O6180.16MonosaccharideC1[C@H]([C@H]([C@@H](C(O1)(CO)O)O)O)O2723872CHEBI:37714
D-GalactoseC6H12O6180.16MonosaccharideC([C@@H]1[C@@H]([C@@H]([C@H](C(O1)O)O)O)O)O6036CHEBI:4139
D-RiboseC5H10O5150.13MonosaccharideC1[C@H]([C@H]([C@H](C(O1)O)O)O)O10975657CHEBI:47006
2-Deoxy-D-riboseC5H10O4134.13MonosaccharideC1[C@@H]([C@H](OC1O)CO)O9828112CHEBI:90761
D-GlucosamineC6H13NO5179.17Amino sugarC([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)N)O)O)O439213CHEBI:47977
N-AcetylglucosamineC8H15NO6221.21Amino sugarCC(=O)N[C@@H](C=O)[C@H]([C@@H]([C@@H](CO)O)O)O1738118CHEBI:17411
Glucuronic acidC6H10O7194.14Sugar acidC(=O)[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O)O)O)O65041CHEBI:47953
InositolC6H12O6180.16Sugar alcoholC1(C(C(C(C(C1O)O)O)O)O)O892CHEBI:24848
SucroseC12H22O11342.30DisaccharideC([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@]2([C@H]([C@@H]([C@H](O2)CO)O)O)CO)O)O)O)O5988CHEBI:17992
MaltoseC12H22O11342.30DisaccharideC([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)O)O)O)O439186CHEBI:17306
LactoseC12H22O11342.30DisaccharideC([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)O)O)O)O440995CHEBI:17716
Glucose 6-phosphateC6H13O9P260.14Glycolysis intermediateC([C@H]([C@H]([C@@H]([C@H](C=O)O)O)O)O)OP(=O)(O)O439958CHEBI:15954
Fructose 6-phosphateC6H13O9P260.14Glycolysis intermediateC([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)OP(=O)(O)O69507CHEBI:15946
Glyceraldehyde 3-phosphateC3H7O6P170.06Glycolysis intermediateC([C@H](C=O)O)OP(=O)(O)O439168CHEBI:29052
Phosphoenolpyruvic acidC3H5O6P168.04Glycolysis intermediateC=C(C(=O)O)OP(=O)(O)O1005CHEBI:44897
Pyruvic acidC3H4O388.06Glycolysis intermediateCC(=O)C(=O)O1060CHEBI:32816
2,3-Bisphosphoglyceric acidC3H8O10P2266.04Glycolysis intermediateC(C(C(=O)O)OP(=O)(O)O)OP(=O)(O)O61CHEBI:28907
Lactic acidC3H6O390.08Fermentation productCC(C(=O)O)O612CHEBI:78320
Ribose 5-phosphateC5H11O8P230.11Pentose phosphate pathway intermediateC([C@H]([C@H]([C@H](C=O)O)O)O)OP(=O)(O)O77982CHEBI:17797
Sedoheptulose 7-phosphateC7H15O10P290.16Pentose phosphate pathway intermediateC([C@H]([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)O)OP(=O)(O)O165007CHEBI:15721
Citric acidC6H8O7192.12TCA cycle intermediateC(C(=O)O)C(CC(=O)O)(C(=O)O)O311CHEBI:30769
Isocitric acidC6H8O7192.12TCA cycle intermediateC(C(C(C(=O)O)O)C(=O)O)C(=O)O1198CHEBI:30887
Alpha-ketoglutaric acidC5H6O5146.10TCA cycle intermediateC(CC(=O)O)C(=O)C(=O)O51CHEBI:30915
Succinic acidC4H6O4118.09TCA cycle intermediateC(CC(=O)O)C(=O)O1110CHEBI:15741
Fumaric acidC4H4O4116.07TCA cycle intermediateC(=C/C(=O)O)\C(=O)O444972CHEBI:18012
Malic acidC4H6O5134.09TCA cycle intermediateC(C(C(=O)O)O)C(=O)O525CHEBI:6650
Oxaloacetic acidC4H4O5132.07TCA cycle intermediateC(C(=O)C(=O)O)C(=O)O970CHEBI:30744
Acetoacetic acidC4H6O3102.09Ketone bodyCC(=O)CC(=O)O96CHEBI:15344
3-Hydroxybutyric acidC4H8O3104.10Ketone bodyCC(CC(=O)O)O441CHEBI:20067
Methylmalonic acidC4H6O4118.09MetaboliteCC(C(=O)O)C(=O)O487CHEBI:30860
CreatineC4H9N3O2131.14MetaboliteCN(CC(=O)O)C(=N)N586CHEBI:16919
CreatinineC4H7N3O113.12Waste productCN1CC(=O)N=C1N588CHEBI:16737
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About this dataset

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, and each one in the table was checked to describe the same structure as the PubChem record.

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

Rows are grouped by biological role: amino acids, nucleobases, nucleosides, nucleotides, cofactors, central-carbon intermediates, lipids, hormones, vitamins, neurotransmitters, and other metabolites. Structures come from PubChem, and a ChEBI ID is included only when ChEBI records the same InChIKey as the PubChem compound. 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.

License and citation

This compilation is free to download and reuse under the Creative Commons Attribution 4.0 International license. Credit ProteinIQ and the original sources when you share it or publish results that use it.

Suggested citation: ProteinIQ (2026). List of biological molecules, version 2026.10.05. https://proteiniq.io/datasets/biological-molecules

Sources and further reading

  • ChEBI: Chemical ontology classes, biological roles, synonyms, formulas, SMILES, InChI, and ChEBI identifiers. ChEBI provides ontology, flat-file, SDF, and SQL downloads from EMBL-EBI.
  • PubChem: Canonical compound identifiers, names, formulas, structures, SMILES, and downloadable compound records. NCBI places no restrictions on PubChem data, though original submitters may retain rights in submitted records.
  • RDKit: Derived descriptors such as molecular weight, LogP, TPSA, hydrogen-bond counts, and canonicalized structures.

Frequently asked questions