# List of biological molecules

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

Rows184

Last updatedOctober 5, 2026

Version2026.10.05

License[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)

FormatsCSV, JSON

SourcesChEBI, PubChem, RDKit

Citation

[CSV](https://proteiniq.io/datasets/biological-molecules/download?format=csv)[JSON](https://proteiniq.io/datasets/biological-molecules/download?format=json)

|  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- |
| Water | H2O | 18.02 | Solvent of life | `O` | [962](https://pubchem.ncbi.nlm.nih.gov/compound/962) | [CHEBI:15377](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15377) |  |
| Glycine | C2H5NO2 | 75.07 | Amino acid | `C(C(=O)O)N` | [750](https://pubchem.ncbi.nlm.nih.gov/compound/750) | [CHEBI:15428](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15428) |  |
| L-Alanine | C3H7NO2 | 89.09 | Amino acid | `C[C@@H](C(=O)O)N` | [5950](https://pubchem.ncbi.nlm.nih.gov/compound/5950) | [CHEBI:16977](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16977) |  |
| L-Valine | C5H11NO2 | 117.15 | Amino acid | `CC(C)[C@@H](C(=O)O)N` | [6287](https://pubchem.ncbi.nlm.nih.gov/compound/6287) | [CHEBI:16414](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16414) |  |
| L-Leucine | C6H13NO2 | 131.18 | Amino acid | `CC(C)C[C@@H](C(=O)O)N` | [6106](https://pubchem.ncbi.nlm.nih.gov/compound/6106) | [CHEBI:15603](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15603) |  |
| L-Isoleucine | C6H13NO2 | 131.18 | Amino acid | `CC[C@H](C)[C@@H](C(=O)O)N` | [6306](https://pubchem.ncbi.nlm.nih.gov/compound/6306) | [CHEBI:17191](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17191) |  |
| L-Proline | C5H9NO2 | 115.13 | Amino acid | `C1C[C@H](NC1)C(=O)O` | [145742](https://pubchem.ncbi.nlm.nih.gov/compound/145742) | [CHEBI:17203](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17203) |  |
| L-Phenylalanine | C9H11NO2 | 165.19 | Amino acid | `C1=CC=C(C=C1)C[C@@H](C(=O)O)N` | [6140](https://pubchem.ncbi.nlm.nih.gov/compound/6140) | [CHEBI:17295](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17295) |  |
| L-Tryptophan | C11H12N2O2 | 204.23 | Amino acid | `C1=CC=C2C(=C1)C(=CN2)C[C@@H](C(=O)O)N` | [6305](https://pubchem.ncbi.nlm.nih.gov/compound/6305) | [CHEBI:16828](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16828) |  |
| L-Tyrosine | C9H11NO3 | 181.19 | Amino acid | `C1=CC(=CC=C1C[C@@H](C(=O)O)N)O` | [6057](https://pubchem.ncbi.nlm.nih.gov/compound/6057) | [CHEBI:17895](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17895) |  |
| L-Serine | C3H7NO3 | 105.09 | Amino acid | `C([C@@H](C(=O)O)N)O` | [5951](https://pubchem.ncbi.nlm.nih.gov/compound/5951) | [CHEBI:17115](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17115) |  |
| L-Threonine | C4H9NO3 | 119.12 | Amino acid | `C[C@H]([C@@H](C(=O)O)N)O` | [6288](https://pubchem.ncbi.nlm.nih.gov/compound/6288) | [CHEBI:16857](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16857) |  |
| L-Cysteine | C3H7NO2S | 121.15 | Amino acid | `C([C@@H](C(=O)O)N)S` | [5862](https://pubchem.ncbi.nlm.nih.gov/compound/5862) | [CHEBI:17561](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17561) |  |
| L-Methionine | C5H11NO2S | 149.21 | Amino acid | `CSCC[C@@H](C(=O)O)N` | [6137](https://pubchem.ncbi.nlm.nih.gov/compound/6137) | [CHEBI:16643](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16643) |  |
| L-Asparagine | C4H8N2O3 | 132.12 | Amino acid | `C([C@@H](C(=O)O)N)C(=O)N` | [6267](https://pubchem.ncbi.nlm.nih.gov/compound/6267) | [CHEBI:17196](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17196) |  |
| L-Glutamine | C5H10N2O3 | 146.15 | Amino acid | `C(CC(=O)N)[C@@H](C(=O)O)N` | [5961](https://pubchem.ncbi.nlm.nih.gov/compound/5961) | [CHEBI:18050](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18050) |  |
| L-Aspartic acid | C4H7NO4 | 133.10 | Amino acid | `C([C@@H](C(=O)O)N)C(=O)O` | [5960](https://pubchem.ncbi.nlm.nih.gov/compound/5960) | [CHEBI:17053](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17053) |  |
| L-Glutamic acid | C5H9NO4 | 147.13 | Amino acid | `C(CC(=O)O)[C@@H](C(=O)O)N` | [33032](https://pubchem.ncbi.nlm.nih.gov/compound/33032) | [CHEBI:16015](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16015) |  |
| L-Lysine | C6H14N2O2 | 146.19 | Amino acid | `C(CCN)C[C@@H](C(=O)O)N` | [5962](https://pubchem.ncbi.nlm.nih.gov/compound/5962) | [CHEBI:18019](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18019) |  |
| L-Arginine | C6H14N4O2 | 174.20 | Amino acid | `C(C[C@@H](C(=O)O)N)CN=C(N)N` | [6322](https://pubchem.ncbi.nlm.nih.gov/compound/6322) | [CHEBI:16467](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16467) |  |
| L-Histidine | C6H9N3O2 | 155.16 | Amino acid | `C1=C(NC=N1)C[C@@H](C(=O)O)N` | [6274](https://pubchem.ncbi.nlm.nih.gov/compound/6274) | [CHEBI:15971](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15971) |  |
| L-Ornithine | C5H12N2O2 | 132.16 | Non-proteinogenic amino acid | `C(C[C@@H](C(=O)O)N)CN` | [6262](https://pubchem.ncbi.nlm.nih.gov/compound/6262) | [CHEBI:15729](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15729) |  |
| L-Citrulline | C6H13N3O3 | 175.19 | Non-proteinogenic amino acid | `C(C[C@@H](C(=O)O)N)CNC(=O)N` | [9750](https://pubchem.ncbi.nlm.nih.gov/compound/9750) | [CHEBI:16349](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16349) |  |
| L-Homocysteine | C4H9NO2S | 135.18 | Non-proteinogenic amino acid | `C(CS)[C@@H](C(=O)O)N` | [91552](https://pubchem.ncbi.nlm.nih.gov/compound/91552) | [CHEBI:17588](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17588) |  |
| Beta-alanine | C3H7NO2 | 89.09 | Non-proteinogenic amino acid | `C(CN)C(=O)O` | [239](https://pubchem.ncbi.nlm.nih.gov/compound/239) | [CHEBI:16958](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16958) |  |
| Taurine | C2H7NO3S | 125.14 | Amino sulfonic acid | `C(CS(=O)(=O)O)N` | [1123](https://pubchem.ncbi.nlm.nih.gov/compound/1123) | [CHEBI:15891](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15891) |  |
| Glutathione | C10H17N3O6S | 307.32 | Peptide | `C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N` | [124886](https://pubchem.ncbi.nlm.nih.gov/compound/124886) | [CHEBI:16856](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16856) |  |
| Carnosine | C9H14N4O3 | 226.24 | Peptide | `C1=C(NC=N1)C[C@@H](C(=O)O)NC(=O)CCN` | [439224](https://pubchem.ncbi.nlm.nih.gov/compound/439224) | [CHEBI:15727](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15727) |  |
| Anserine | C10H16N4O3 | 240.26 | Peptide | `CN1C=NC=C1C[C@@H](C(=O)O)NC(=O)CCN` | [112072](https://pubchem.ncbi.nlm.nih.gov/compound/112072) | [CHEBI:18323](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18323) |  |
| Adenine | C5H5N5 | 135.13 | Nucleobase | `C1=NC2=NC=NC(=C2N1)N` | [190](https://pubchem.ncbi.nlm.nih.gov/compound/190) | [CHEBI:16708](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16708) |  |
| Guanine | C5H5N5O | 151.13 | Nucleobase | `C1=NC2=C(N1)C(=O)NC(=N2)N` | [135398634](https://pubchem.ncbi.nlm.nih.gov/compound/135398634) | [CHEBI:16235](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16235) |  |
| Cytosine | C4H5N3O | 111.10 | Nucleobase | `C1=C(NC(=O)N=C1)N` | [597](https://pubchem.ncbi.nlm.nih.gov/compound/597) | [CHEBI:16040](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16040) |  |
| Thymine | C5H6N2O2 | 126.12 | Nucleobase | `CC1=CNC(=O)NC1=O` | [1135](https://pubchem.ncbi.nlm.nih.gov/compound/1135) | [CHEBI:17821](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17821) |  |
| Uracil | C4H4N2O2 | 112.09 | Nucleobase | `C1=CNC(=O)NC1=O` | [1174](https://pubchem.ncbi.nlm.nih.gov/compound/1174) | [CHEBI:17568](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17568) |  |
| Adenosine | C10H13N5O4 | 267.25 | Nucleoside | `C1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N` | [60961](https://pubchem.ncbi.nlm.nih.gov/compound/60961) | [CHEBI:16335](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16335) |  |
| Guanosine | C10H13N5O5 | 283.24 | Nucleoside | `C1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N` | [135398635](https://pubchem.ncbi.nlm.nih.gov/compound/135398635) | [CHEBI:16750](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16750) |  |
| Cytidine | C9H13N3O5 | 243.22 | Nucleoside | `C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O` | [6175](https://pubchem.ncbi.nlm.nih.gov/compound/6175) | [CHEBI:17562](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17562) |  |
| Uridine | C9H12N2O6 | 244.20 | Nucleoside | `C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O` | [6029](https://pubchem.ncbi.nlm.nih.gov/compound/6029) | [CHEBI:16704](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16704) |  |
| Inosine | C10H12N4O5 | 268.23 | Nucleoside | `C1=NC2=C(C(=O)N1)N=CN2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O` | [135398641](https://pubchem.ncbi.nlm.nih.gov/compound/135398641) | [CHEBI:17596](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17596) |  |
| Xanthosine | C10H12N4O6 | 284.23 | Nucleoside | `C1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)NC(=O)NC2=O` | [64959](https://pubchem.ncbi.nlm.nih.gov/compound/64959) | [CHEBI:18107](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18107) |  |
| Deoxyadenosine | C10H13N5O3 | 251.25 | Nucleoside | `C1[C@@H]([C@H](O[C@H]1N2C=NC3=C(N=CN=C32)N)CO)O` | [13730](https://pubchem.ncbi.nlm.nih.gov/compound/13730) | [CHEBI:17256](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17256) |  |
| Deoxyguanosine | C10H13N5O4 | 267.25 | Nucleoside | `C1[C@@H]([C@H](O[C@H]1N2C=NC3=C2N=C(NC3=O)N)CO)O` | [135398592](https://pubchem.ncbi.nlm.nih.gov/compound/135398592) | [CHEBI:17172](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17172) |  |
| Deoxycytidine | C9H13N3O4 | 227.22 | Nucleoside | `C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO)O` | [13711](https://pubchem.ncbi.nlm.nih.gov/compound/13711) | [CHEBI:15698](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15698) |  |
| Thymidine | C10H14N2O5 | 242.23 | Nucleoside | `CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O` | [5789](https://pubchem.ncbi.nlm.nih.gov/compound/5789) | [CHEBI:17748](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17748) |  |
| Adenosine triphosphate | C10H16N5O13P3 | 507.18 | Nucleotide | `C1=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)N` | [5957](https://pubchem.ncbi.nlm.nih.gov/compound/5957) | [CHEBI:15422](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15422) |  |
| Adenosine diphosphate | C10H15N5O10P2 | 427.20 | Nucleotide | `C1=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)N` | [6022](https://pubchem.ncbi.nlm.nih.gov/compound/6022) | [CHEBI:16761](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16761) |  |
| Adenosine monophosphate | C10H14N5O7P | 347.22 | Nucleotide | `C1=NC(=C2C(=N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N` | [6083](https://pubchem.ncbi.nlm.nih.gov/compound/6083) | [CHEBI:16027](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16027) |  |
| Guanosine monophosphate | C10H14N5O8P | 363.22 | Nucleotide | `C1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N` | [135398631](https://pubchem.ncbi.nlm.nih.gov/compound/135398631) | [CHEBI:17345](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17345) |  |
| Cytidine monophosphate | C9H14N3O8P | 323.20 | Nucleotide | `C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O` | [6131](https://pubchem.ncbi.nlm.nih.gov/compound/6131) | [CHEBI:17361](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17361) |  |
| Uridine monophosphate | C9H13N2O9P | 324.18 | Nucleotide | `C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O` | [6030](https://pubchem.ncbi.nlm.nih.gov/compound/6030) | [CHEBI:16695](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16695) |  |
| Deoxyadenosine monophosphate | C10H14N5O6P | 331.23 | Nucleotide | `C1[C@@H]([C@H](O[C@H]1N2C=NC3=C(N=CN=C32)N)COP(=O)(O)O)O` | [12599](https://pubchem.ncbi.nlm.nih.gov/compound/12599) | [CHEBI:17713](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17713) |  |
| Deoxyguanosine monophosphate | C10H14N5O7P | 347.22 | Nucleotide | `C1[C@@H]([C@H](O[C@H]1N2C=NC3=C2N=C(NC3=O)N)COP(=O)(O)O)O` | [135398597](https://pubchem.ncbi.nlm.nih.gov/compound/135398597) | [CHEBI:16192](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16192) |  |
| Thymidine monophosphate | C10H15N2O8P | 322.21 | Nucleotide | `CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O` | [9700](https://pubchem.ncbi.nlm.nih.gov/compound/9700) | [CHEBI:17013](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17013) |  |
| Orotidine monophosphate | C10H13N2O11P | 368.19 | Nucleotide | `C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C(=O)O` | [160617](https://pubchem.ncbi.nlm.nih.gov/compound/160617) | [CHEBI:15842](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15842) |  |
| Nicotinamide mononucleotide | C11H15N2O8P | 334.22 | Nucleotide | `C1=CC(=C[N+](=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)[O-])O)O)C(=O)N` | [14180](https://pubchem.ncbi.nlm.nih.gov/compound/14180) | [CHEBI:16171](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16171) |  |
| Nicotinamide adenine dinucleotide (NAD+) | C21H27N7O14P2 | 663.43 | Cofactor | `C1=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)N` | [5892](https://pubchem.ncbi.nlm.nih.gov/compound/5892) | [CHEBI:44215](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:44215) |  |
| NADH | C21H29N7O14P2 | 665.45 | Cofactor | `C1C=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)O` | [439153](https://pubchem.ncbi.nlm.nih.gov/compound/439153) | [CHEBI:16908](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16908) |  |
| NADP+ | C21H28N7O17P3 | 743.41 | Cofactor | `C1=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)N` | [5885](https://pubchem.ncbi.nlm.nih.gov/compound/5885) | [CHEBI:44409](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:44409) |  |
| NADPH | C21H30N7O17P3 | 745.43 | Cofactor | `C1C=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)O` | [5884](https://pubchem.ncbi.nlm.nih.gov/compound/5884) | [CHEBI:16474](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16474) |  |
| Flavin adenine dinucleotide | C27H33N9O15P2 | 785.56 | Cofactor | `CC1=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)O` | [643975](https://pubchem.ncbi.nlm.nih.gov/compound/643975) | [CHEBI:16238](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16238) |  |
| Flavin mononucleotide | C17H21N4O9P | 456.35 | Cofactor | `CC1=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)O` | [643976](https://pubchem.ncbi.nlm.nih.gov/compound/643976) | [CHEBI:17621](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17621) |  |
| Coenzyme A | C21H36N7O16P3S | 767.53 | Cofactor | `CC(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)O` | [87642](https://pubchem.ncbi.nlm.nih.gov/compound/87642) | [CHEBI:15346](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15346) |  |
| Acetyl-CoA | C23H38N7O17P3S | 809.57 | Cofactor | `CC(=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)O` | [444493](https://pubchem.ncbi.nlm.nih.gov/compound/444493) | [CHEBI:15351](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15351) |  |
| S-Adenosylmethionine | C15H22N6O5S | 398.44 | Cofactor | `C[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)O` | [34755](https://pubchem.ncbi.nlm.nih.gov/compound/34755) | [CHEBI:67040](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:67040) |  |
| S-Adenosylhomocysteine | C14H20N6O5S | 384.41 | Metabolite | `C1=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)N` | [439155](https://pubchem.ncbi.nlm.nih.gov/compound/439155) | [CHEBI:16680](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16680) |  |
| Lipoic acid | C8H14O2S2 | 206.32 | Cofactor | `C1CSS[C@@H]1CCCCC(=O)O` | [6112](https://pubchem.ncbi.nlm.nih.gov/compound/6112) | [CHEBI:30314](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30314) |  |
| Heme | C34H32FeN4O4 | 616.50 | Cofactor | `CC1=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](https://pubchem.ncbi.nlm.nih.gov/compound/26945) | - |  |
| D-Glucose | C6H12O6 | 180.16 | Monosaccharide | `C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O` | [5793](https://pubchem.ncbi.nlm.nih.gov/compound/5793) | [CHEBI:4167](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:4167) |  |
| D-Fructose | C6H12O6 | 180.16 | Monosaccharide | `C1[C@H]([C@H]([C@@H](C(O1)(CO)O)O)O)O` | [2723872](https://pubchem.ncbi.nlm.nih.gov/compound/2723872) | [CHEBI:37714](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37714) |  |
| D-Galactose | C6H12O6 | 180.16 | Monosaccharide | `C([C@@H]1[C@@H]([C@@H]([C@H](C(O1)O)O)O)O)O` | [6036](https://pubchem.ncbi.nlm.nih.gov/compound/6036) | [CHEBI:4139](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:4139) |  |
| D-Ribose | C5H10O5 | 150.13 | Monosaccharide | `C1[C@H]([C@H]([C@H](C(O1)O)O)O)O` | [10975657](https://pubchem.ncbi.nlm.nih.gov/compound/10975657) | [CHEBI:47006](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47006) |  |
| 2-Deoxy-D-ribose | C5H10O4 | 134.13 | Monosaccharide | `C1[C@@H]([C@H](OC1O)CO)O` | [9828112](https://pubchem.ncbi.nlm.nih.gov/compound/9828112) | [CHEBI:90761](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:90761) |  |
| D-Glucosamine | C6H13NO5 | 179.17 | Amino sugar | `C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)N)O)O)O` | [439213](https://pubchem.ncbi.nlm.nih.gov/compound/439213) | [CHEBI:47977](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47977) |  |
| N-Acetylglucosamine | C8H15NO6 | 221.21 | Amino sugar | `CC(=O)N[C@@H](C=O)[C@H]([C@@H]([C@@H](CO)O)O)O` | [1738118](https://pubchem.ncbi.nlm.nih.gov/compound/1738118) | [CHEBI:17411](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17411) |  |
| Glucuronic acid | C6H10O7 | 194.14 | Sugar acid | `C(=O)[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O)O)O)O` | [65041](https://pubchem.ncbi.nlm.nih.gov/compound/65041) | [CHEBI:47953](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47953) |  |
| Inositol | C6H12O6 | 180.16 | Sugar alcohol | `C1(C(C(C(C(C1O)O)O)O)O)O` | [892](https://pubchem.ncbi.nlm.nih.gov/compound/892) | [CHEBI:24848](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24848) |  |
| Sucrose | C12H22O11 | 342.30 | Disaccharide | `C([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)O` | [5988](https://pubchem.ncbi.nlm.nih.gov/compound/5988) | [CHEBI:17992](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17992) |  |
| Maltose | C12H22O11 | 342.30 | Disaccharide | `C([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)O` | [439186](https://pubchem.ncbi.nlm.nih.gov/compound/439186) | [CHEBI:17306](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17306) |  |
| Lactose | C12H22O11 | 342.30 | Disaccharide | `C([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)O` | [440995](https://pubchem.ncbi.nlm.nih.gov/compound/440995) | [CHEBI:17716](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17716) |  |
| Glucose 6-phosphate | C6H13O9P | 260.14 | Glycolysis intermediate | `C([C@H]([C@H]([C@@H]([C@H](C=O)O)O)O)O)OP(=O)(O)O` | [439958](https://pubchem.ncbi.nlm.nih.gov/compound/439958) | [CHEBI:15954](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15954) |  |
| Fructose 6-phosphate | C6H13O9P | 260.14 | Glycolysis intermediate | `C([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)OP(=O)(O)O` | [69507](https://pubchem.ncbi.nlm.nih.gov/compound/69507) | [CHEBI:15946](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15946) |  |
| Glyceraldehyde 3-phosphate | C3H7O6P | 170.06 | Glycolysis intermediate | `C([C@H](C=O)O)OP(=O)(O)O` | [439168](https://pubchem.ncbi.nlm.nih.gov/compound/439168) | [CHEBI:29052](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29052) |  |
| Phosphoenolpyruvic acid | C3H5O6P | 168.04 | Glycolysis intermediate | `C=C(C(=O)O)OP(=O)(O)O` | [1005](https://pubchem.ncbi.nlm.nih.gov/compound/1005) | [CHEBI:44897](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:44897) |  |
| Pyruvic acid | C3H4O3 | 88.06 | Glycolysis intermediate | `CC(=O)C(=O)O` | [1060](https://pubchem.ncbi.nlm.nih.gov/compound/1060) | [CHEBI:32816](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32816) |  |
| 2,3-Bisphosphoglyceric acid | C3H8O10P2 | 266.04 | Glycolysis intermediate | `C(C(C(=O)O)OP(=O)(O)O)OP(=O)(O)O` | [61](https://pubchem.ncbi.nlm.nih.gov/compound/61) | [CHEBI:28907](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28907) |  |
| Lactic acid | C3H6O3 | 90.08 | Fermentation product | `CC(C(=O)O)O` | [612](https://pubchem.ncbi.nlm.nih.gov/compound/612) | [CHEBI:78320](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:78320) |  |
| Ribose 5-phosphate | C5H11O8P | 230.11 | Pentose phosphate pathway intermediate | `C([C@H]([C@H]([C@H](C=O)O)O)O)OP(=O)(O)O` | [77982](https://pubchem.ncbi.nlm.nih.gov/compound/77982) | [CHEBI:17797](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17797) |  |
| Sedoheptulose 7-phosphate | C7H15O10P | 290.16 | Pentose phosphate pathway intermediate | `C([C@H]([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)O)OP(=O)(O)O` | [165007](https://pubchem.ncbi.nlm.nih.gov/compound/165007) | [CHEBI:15721](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15721) |  |
| Citric acid | C6H8O7 | 192.12 | TCA cycle intermediate | `C(C(=O)O)C(CC(=O)O)(C(=O)O)O` | [311](https://pubchem.ncbi.nlm.nih.gov/compound/311) | [CHEBI:30769](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30769) |  |
| Isocitric acid | C6H8O7 | 192.12 | TCA cycle intermediate | `C(C(C(C(=O)O)O)C(=O)O)C(=O)O` | [1198](https://pubchem.ncbi.nlm.nih.gov/compound/1198) | [CHEBI:30887](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30887) |  |
| Alpha-ketoglutaric acid | C5H6O5 | 146.10 | TCA cycle intermediate | `C(CC(=O)O)C(=O)C(=O)O` | [51](https://pubchem.ncbi.nlm.nih.gov/compound/51) | [CHEBI:30915](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30915) |  |
| Succinic acid | C4H6O4 | 118.09 | TCA cycle intermediate | `C(CC(=O)O)C(=O)O` | [1110](https://pubchem.ncbi.nlm.nih.gov/compound/1110) | [CHEBI:15741](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15741) |  |
| Fumaric acid | C4H4O4 | 116.07 | TCA cycle intermediate | `C(=C/C(=O)O)\C(=O)O` | [444972](https://pubchem.ncbi.nlm.nih.gov/compound/444972) | [CHEBI:18012](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18012) |  |
| Malic acid | C4H6O5 | 134.09 | TCA cycle intermediate | `C(C(C(=O)O)O)C(=O)O` | [525](https://pubchem.ncbi.nlm.nih.gov/compound/525) | [CHEBI:6650](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:6650) |  |
| Oxaloacetic acid | C4H4O5 | 132.07 | TCA cycle intermediate | `C(C(=O)C(=O)O)C(=O)O` | [970](https://pubchem.ncbi.nlm.nih.gov/compound/970) | [CHEBI:30744](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30744) |  |
| Acetoacetic acid | C4H6O3 | 102.09 | Ketone body | `CC(=O)CC(=O)O` | [96](https://pubchem.ncbi.nlm.nih.gov/compound/96) | [CHEBI:15344](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15344) |  |
| 3-Hydroxybutyric acid | C4H8O3 | 104.10 | Ketone body | `CC(CC(=O)O)O` | [441](https://pubchem.ncbi.nlm.nih.gov/compound/441) | [CHEBI:20067](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:20067) |  |
| Methylmalonic acid | C4H6O4 | 118.09 | Metabolite | `CC(C(=O)O)C(=O)O` | [487](https://pubchem.ncbi.nlm.nih.gov/compound/487) | [CHEBI:30860](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30860) |  |
| Creatine | C4H9N3O2 | 131.14 | Metabolite | `CN(CC(=O)O)C(=N)N` | [586](https://pubchem.ncbi.nlm.nih.gov/compound/586) | [CHEBI:16919](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16919) |  |
| Creatinine | C4H7N3O | 113.12 | Waste product | `CN1CC(=O)N=C1N` | [588](https://pubchem.ncbi.nlm.nih.gov/compound/588) | [CHEBI:16737](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI: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](https://creativecommons.org/licenses/by/4.0/) 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](https://www.ebi.ac.uk/chebi/downloadsForward.do): 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](https://pubchem.ncbi.nlm.nih.gov/): 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](https://www.rdkit.org/): Derived descriptors such as molecular weight, LogP, TPSA, hydrogen-bond counts, and canonicalized structures.

## Frequently asked questions