List of biological molecules

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

CSVJSON
NameFormulaMW (g/mol)Biological classSMILESPubChem CIDChEBI ID
WaterH2O18.02SolventO962CHEBI:15377
D-GlucoseC6H12O6180.16CarbohydrateC([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O5793CHEBI:17234
GlycineC2H5NO275.07Amino acidC(C(=O)O)N750CHEBI:15428
AdenineC5H5N5135.13NucleobaseC1=NC2=C(N1)N=CN=C2N190CHEBI:16708
Adenosine triphosphateC10H16N5O13P3507.18Cofactor / nucleotideC1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O5957CHEBI:15422
CholesterolC27H46O386.66Sterol lipidCC(C)CCCC(C)C1CCC2C1(CCC3C2CCC4=CC(O)CCC34C)C5997CHEBI:16113
Lactic acidC3H6O390.08MetaboliteCC(C(=O)O)O612CHEBI:28358
Citric acidC6H8O7192.12Central-carbon metaboliteC(C(=O)O)C(CC(=O)O)(C(=O)O)O311CHEBI:30769
Palmitic acidC16H32O2256.43Fatty acidCCCCCCCCCCCCCCCC(=O)O985CHEBI:15756
DopamineC8H11NO2153.18NeurotransmitterC1=CC(=C(C=C1CCN)O)O681CHEBI:18243
L-AlanineC3H7NO289.09Amino acidC[C@@H](C(=O)O)N5950CHEBI:16977
L-ValineC5H11NO2117.15Amino acidCC(C)[C@@H](C(=O)O)N6287CHEBI:16414
L-SerineC3H7NO3105.09Amino acidC([C@@H](C(=O)O)N)O5951CHEBI:17115
UracilC4H4N2O2112.09NucleobaseC1=CNC(=O)NC1=O1174CHEBI:17568
CytosineC4H5N3O111.10NucleobaseC1=C(NC(=O)N=C1)N597CHEBI:16040
GuanineC5H5N5O151.13NucleobaseC1=NC2=C(N1)C(=O)NC(=N2)N135398634CHEBI:16235
ThymineC5H6N2O2126.12NucleobaseCC1=CNC(=O)NC1=O1135CHEBI:17821
Pyruvic acidC3H4O388.06Central-carbon metaboliteCC(=O)C(=O)O1060CHEBI:15361
FructoseC6H12O6180.16CarbohydrateC1[C@H]([C@H]([C@@H](C(O1)(CO)O)O)O)O2723872-
RiboseC5H10O5150.13CarbohydrateC1[C@H]([C@H]([C@H](C(O1)O)O)O)O10975657-
GalactoseC6H12O6180.16CarbohydrateC([C@@H]1[C@@H]([C@@H]([C@H](C(O1)O)O)O)O)O6036-
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)O5988-
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)O439186-
LysineC6H14N2O2146.19Amino acidC(CCN)C[C@@H](C(=O)O)N5962-
Glutamic acidC5H9NO4147.13Amino acidC(CC(=O)O)[C@@H](C(=O)O)N33032-
Aspartic acidC4H7NO4133.10Amino acidC([C@@H](C(=O)O)N)C(=O)O5960-
PhenylalanineC9H11NO2165.19Amino acidC1=CC=C(C=C1)C[C@@H](C(=O)O)N6140-
TryptophanC11H12N2O2204.23Amino acidC1=CC=C2C(=C1)C(=CN2)C[C@@H](C(=O)O)N6305-
TyrosineC9H11NO3181.19Amino acidC1=CC(=CC=C1C[C@@H](C(=O)O)N)O6057-
CysteineC3H7NO2S121.15Amino acidC([C@@H](C(=O)O)N)S5862-
MethionineC5H11NO2S149.21Amino acidCSCC[C@@H](C(=O)O)N6137-
HistidineC6H9N3O2155.16Amino acidC1=C(NC=N1)C[C@@H](C(=O)O)N6274-
ProlineC5H9NO2115.13Amino acidC1C[C@H](NC1)C(=O)O145742-
ArginineC6H14N4O2174.20Amino acidC(C[C@@H](C(=O)O)N)CN=C(N)N6322-
AsparagineC4H8N2O3132.12Amino acidC([C@@H](C(=O)O)N)C(=O)N6267-
GlutamineC5H10N2O3146.15Amino acidC(CC(=O)N)[C@@H](C(=O)O)N5961-
CreatineC4H9N3O2131.14MetaboliteCN(CC(=O)O)C(=N)N586-
GlutathioneC10H17N3O6S307.32Peptide antioxidantC(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N124886-
SerotoninC10H12N2O176.22NeurotransmitterC1=CC2=C(C=C1O)C(=CN2)CCN5202-
EpinephrineC9H13NO3183.21Hormone / neurotransmitterCNC[C@@H](C1=CC(=C(C=C1)O)O)O5816-
MelatoninC13H16N2O2232.28HormoneCC(=O)NCCC1=CNC2=C1C=C(C=C2)OC896-
Ascorbic acidC6H8O6176.12VitaminC([C@@H]([C@@H]1C(=C(C(=O)O1)O)O)O)O54670067-
RiboflavinC17H20N4O6376.37VitaminCC1=CC2=C(C=C1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO)O)O)O493570-
DeoxyriboseC5H10O4134.13Biological moleculeC1[C@@H]([C@H](OC1O)CO)O9828112-
LactoseC12H22O11342.30Biological moleculeC([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)O440995-
GlycogenC24H42O21666.58Biological moleculeC([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OC[C@@H]2[C@H]([C@@H]([C@H]([C@H](O2)O[C@@H]3[C@H](O[C@@H]([C@@H]([C@H]3O)O)O)CO)O)O)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O)O)O439177-
LeucineC6H13NO2131.18Biological moleculeCC(C)C[C@@H](C(=O)O)N6106-
IsoleucineC6H13NO2131.18Biological moleculeCC[C@H](C)[C@@H](C(=O)O)N6306-
ThreonineC4H9NO3119.12Biological moleculeC[C@H]([C@@H](C(=O)O)N)O6288-
AdenosineC10H13N5O4267.25Biological moleculeC1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N60961-
GuanosineC10H13N5O5283.24Biological moleculeC1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N135398635-
CytidineC9H13N3O5243.22Biological moleculeC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O6175-
UridineC9H12N2O6244.20Biological moleculeC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O6029-
Adenosine DiphosphateC10H15N5O10P2427.20Biological moleculeC1=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)N6022-
Adenosine MonophosphateC10H14N5O7P347.22Biological moleculeC1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N6083-
Nicotinamide Adenine DinucleotideC21H27N7O14P2663.43Biological moleculeC1=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)N5892-
Flavin Adenine DinucleotideC27H33N9O15P2785.56Biological moleculeCC1=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)O643975-
Coenzyme AC21H36N7O16P3S767.53Biological moleculeCC(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)O87642-
Isocitric AcidC6H8O7192.12Biological moleculeC(C(C(C(=O)O)O)C(=O)O)C(=O)O1198-
Alpha-Ketoglutaric AcidC5H6O5146.10Biological moleculeC(CC(=O)O)C(=O)C(=O)O51-
Succinic AcidC4H6O4118.09Biological moleculeC(CC(=O)O)C(=O)O1110-
Fumaric AcidC4H4O4116.07Biological moleculeC(=C/C(=O)O)\C(=O)O444972-
Malic AcidC4H6O5134.09Biological moleculeC(C(C(=O)O)O)C(=O)O525-
Oxaloacetic AcidC4H4O5132.07Biological moleculeC(C(=O)C(=O)O)C(=O)O970-
Acetyl-CoAC23H38N7O17P3S809.57Biological moleculeCC(=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)O444493-
CreatinineC4H7N3O113.12Biological moleculeCN1CC(=O)N=C1N588-
UreaCH4N2O60.06Biological moleculeC(=O)(N)N1176-
Uric AcidC5H4N4O3168.11Biological moleculeC12=C(NC(=O)N1)NC(=O)NC2=O1175-
Stearic AcidC18H36O2284.48Biological moleculeCCCCCCCCCCCCCCCCCC(=O)O5281-
Oleic AcidC18H34O2282.47Biological moleculeCCCCCCCC/C=C\CCCCCCCC(=O)O445639-
Linoleic AcidC18H32O2280.45Biological moleculeCCCCC/C=C\C/C=C\CCCCCCCC(=O)O5280450-
Linolenic AcidC18H30O2278.44Biological moleculeCC/C=C\C/C=C\C/C=C\CCCCCCCC(=O)O5280934-
Arachidonic AcidC20H32O2304.47Biological moleculeCCCCC/C=C\C/C=C\C/C=C\C/C=C\CCCC(=O)O444899-
Docosahexaenoic AcidC22H32O2328.50Biological moleculeCC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCC(=O)O445580-
Eicosapentaenoic AcidC20H30O2302.46Biological moleculeCC/C=C/C/C=C/C/C=C/C/C=C/C/C=C/CCCC(=O)O5282847-
GlycerolC3H8O392.09Biological moleculeC(C(CO)O)O753-
SphingosineC18H37NO2299.50Biological moleculeCCCCCCCCCCCCC/C=C/[C@H]([C@H](CO)N)O5280335-
NorepinephrineC8H11NO3169.18Biological moleculeC1=CC(=C(C=C1[C@H](CN)O)O)O439260-
HistamineC5H9N3111.15Biological moleculeC1=C(NC=N1)CCN774-
AcetylcholineC7H16NO2+146.21Biological moleculeCC(=O)OCC[N+](C)(C)C187-
Gamma-Aminobutyric AcidC4H9NO2103.12Biological moleculeC(CC(=O)O)CN119-
NiacinC6H5NO2123.11Biological moleculeC1=CC(=CN=C1)C(=O)O938-
PyridoxineC8H11NO3169.18Biological moleculeCC1=NC=C(C(=C1O)CO)CO1054-
Folic AcidC19H19N7O6441.40Biological moleculeC1=CC(=CC=C1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCC2=CN=C3C(=N2)C(=O)NC(=N3)N135398658-
BiotinC10H16N2O3S244.31Biological moleculeC1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2171548-
ThiamineC12H17N4OS+265.36Biological moleculeCC1=C(SC=[N+]1CC2=CN=C(N=C2N)C)CCO1130-
RetinolC20H30O286.46Biological moleculeCC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/CO)/C)/C445354-
CholecalciferolC27H44O384.65Biological moleculeC[C@H](CCCC(C)C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C/3\C[C@H](CCC3=C)O)C5280795-
TocopherolC28H48O2416.69Biological moleculeCC1=C(C=C2CCC(OC2=C1C)(C)CCCC(C)CCCC(C)CCCC(C)C)O14986-
PhylloquinoneC31H46O2450.71Biological moleculeCC1=C(C(=O)C2=CC=CC=C2C1=O)C/C=C(\C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C5284607-
HemeC34H32FeN4O4616.50Biological moleculeCC1=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-
BilirubinC33H36N4O6584.67Biological moleculeCC1=C(NC(=C1CCC(=O)O)CC2=C(C(=C(N2)/C=C\3/C(=C(C(=O)N3)C)C=C)C)CCC(=O)O)/C=C\4/C(=C(C(=O)N4)C=C)C5280352-
BiliverdinC33H34N4O6582.66Biological moleculeCC\1=C(/C(=C/C2=C(C(=C(N2)/C=C\3/C(=C(C(=O)N3)C)C=C)C)CCC(=O)O)/N/C1=C\C4=NC(=O)C(=C4C)C=C)CCC(=O)O5280353-
CortisolC21H30O5362.47Biological moleculeC[C@]12CCC(=O)C=C1CC[C@@H]3[C@@H]2[C@H](C[C@]4([C@H]3CC[C@@]4(C(=O)CO)O)C)O5754-
TestosteroneC19H28O2288.43Biological moleculeC[C@]12CC[C@H]3[C@H]([C@@H]1CC[C@@H]2O)CCC4=CC(=O)CC[C@]34C6013-
EstradiolC18H24O2272.39Biological moleculeC[C@]12CC[C@H]3[C@H]([C@@H]1CC[C@@H]2O)CCC4=C3C=CC(=C4)O5757-
ProgesteroneC21H30O2314.47Biological moleculeCC(=O)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4=CC(=O)CC[C@]34C)C5994-
AldosteroneC21H28O5360.45Biological moleculeC[C@]12CCC(=O)C=C1CC[C@@H]3[C@@H]2[C@H](C[C@]4([C@H]3CC[C@@H]4C(=O)CO)C=O)O5839-
ThyroxineC15H11I4NO4776.86Biological moleculeC1=C(C=C(C(=C1I)OC2=CC(=C(C(=C2)I)O)I)I)C[C@@H](C(=O)O)N5819-
TriiodothyronineC15H12I3NO4650.96Biological moleculeC1=CC(=C(C=C1OC2=C(C=C(C=C2I)C[C@@H](C(=O)O)N)I)I)O5920-
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Methodology

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.

Sources

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.

Related datasets

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