accession stringlengths 11 11 | version stringclasses 1
value | name stringlengths 1 255 | smiles stringlengths 1 1.42k ⌀ | inchi stringlengths 10 2.98k ⌀ | inchikey stringlengths 27 27 ⌀ | chemical_formula stringlengths 1 27 ⌀ | status stringclasses 4
values | creation_date stringlengths 23 23 | update_date stringlengths 23 23 | source_record_json stringlengths 1.65k 6.2M |
|---|---|---|---|---|---|---|---|---|---|---|
HMDB0000001 | 5.0 | 1-Methylhistidine | CN1C=NC(C[C@H](N)C(O)=O)=C1 | InChI=1S/C7H11N3O2/c1-10-3-5(9-4-10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12)/t6-/m0/s1 | BRMWTNUJHUMWMS-LURJTMIESA-N | C7H11N3O2 | quantified | 2005-11-16 15:48:42 UTC | 2021-10-13 17:34:04 UTC | {"version": "5.0", "creation_date": "2005-11-16 15:48:42 UTC", "update_date": "2021-10-13 17:34:04 UTC", "accession": "HMDB0000001", "status": "quantified", "secondary_accessions": {"accession": ["HMDB00001", "HMDB0004935", "HMDB0006703", "HMDB0006704", "HMDB04935", "HMDB06703", "HMDB06704"]}, "name": "1-Methylhistidin... |
HMDB0000002 | 5.0 | 1,3-Diaminopropane | NCCCN | InChI=1S/C3H10N2/c4-2-1-3-5/h1-5H2 | XFNJVJPLKCPIBV-UHFFFAOYSA-N | C3H10N2 | quantified | 2005-11-16 15:48:42 UTC | 2021-10-13 04:18:52 UTC | {"version": "5.0", "creation_date": "2005-11-16 15:48:42 UTC", "update_date": "2021-10-13 04:18:52 UTC", "accession": "HMDB0000002", "status": "quantified", "secondary_accessions": {"accession": ["HMDB00002", "HMDB0060172", "HMDB60172"]}, "name": "1,3-Diaminopropane", "synonyms": {"synonym": ["1,3-Propanediamine", "1,3... |
HMDB0000005 | 5.0 | 2-Ketobutyric acid | CCC(=O)C(O)=O | InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7) | TYEYBOSBBBHJIV-UHFFFAOYSA-N | C4H6O3 | quantified | 2005-11-16 15:48:42 UTC | 2020-11-09 23:11:34 UTC | {"version": "5.0", "creation_date": "2005-11-16 15:48:42 UTC", "update_date": "2020-11-09 23:11:34 UTC", "accession": "HMDB0000005", "status": "quantified", "secondary_accessions": {"accession": ["HMDB00005", "HMDB0006544", "HMDB06544"]}, "name": "2-Ketobutyric acid", "synonyms": {"synonym": ["2-Ketobutanoic acid", "2-... |
HMDB0000008 | 5.0 | 2-Hydroxybutyric acid | CC[C@H](O)C(O)=O | InChI=1S/C4H8O3/c1-2-3(5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m0/s1 | AFENDNXGAFYKQO-VKHMYHEASA-N | C4H8O3 | quantified | 2005-11-16 15:48:42 UTC | 2021-09-14 15:44:51 UTC | "{\"version\": \"5.0\", \"creation_date\": \"2005-11-16 15:48:42 UTC\", \"update_date\": \"2021-09-1(...TRUNCATED) |
HMDB0000010 | 5.0 | 2-Methoxyestrone | [H][C@@]12CCC(=O)[C@@]1(C)CC[C@]1([H])C3=C(CC[C@@]21[H])C=C(O)C(OC)=C3 | "InChI=1S/C19H24O3/c1-19-8-7-12-13(15(19)5-6-18(19)21)4-3-11-9-16(20)17(22-2)10-14(11)12/h9-10,12-13(...TRUNCATED) | WHEUWNKSCXYKBU-QPWUGHHJSA-N | C19H24O3 | quantified | 2005-11-16 15:48:42 UTC | 2021-09-14 15:41:25 UTC | "{\"version\": \"5.0\", \"creation_date\": \"2005-11-16 15:48:42 UTC\", \"update_date\": \"2021-09-1(...TRUNCATED) |
HMDB0000011 | 5.0 | 3-Hydroxybutyric acid | C[C@@H](O)CC(O)=O | InChI=1S/C4H8O3/c1-3(5)2-4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1 | WHBMMWSBFZVSSR-GSVOUGTGSA-N | C4H8O3 | quantified | 2005-11-16 15:48:42 UTC | 2021-09-14 15:00:08 UTC | "{\"version\": \"5.0\", \"creation_date\": \"2005-11-16 15:48:42 UTC\", \"update_date\": \"2021-09-1(...TRUNCATED) |
HMDB0000012 | 5.0 | Deoxyuridine | OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O | "InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15(...TRUNCATED) | MXHRCPNRJAMMIM-SHYZEUOFSA-N | C9H12N2O5 | quantified | 2005-11-16 15:48:42 UTC | 2021-09-14 15:44:42 UTC | "{\"version\": \"5.0\", \"creation_date\": \"2005-11-16 15:48:42 UTC\", \"update_date\": \"2021-09-1(...TRUNCATED) |
HMDB0000014 | 5.0 | Deoxycytidine | NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1 | "InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15(...TRUNCATED) | CKTSBUTUHBMZGZ-SHYZEUOFSA-N | C9H13N3O4 | quantified | 2005-11-16 15:48:42 UTC | 2021-09-14 15:48:16 UTC | "{\"version\": \"5.0\", \"creation_date\": \"2005-11-16 15:48:42 UTC\", \"update_date\": \"2021-09-1(...TRUNCATED) |
HMDB0000015 | 5.0 | Cortexolone | [H][C@@]12CC[C@](O)(C(=O)CO)[C@@]1(C)CC[C@@]1([H])[C@@]2([H])CCC2=CC(=O)CC[C@]12C | "InChI=1S/C21H30O4/c1-19-8-5-14(23)11-13(19)3-4-15-16(19)6-9-20(2)17(15)7-10-21(20,25)18(24)12-22/h1(...TRUNCATED) | WHBHBVVOGNECLV-OBQKJFGGSA-N | C21H30O4 | quantified | 2005-11-16 15:48:42 UTC | 2021-09-14 15:40:02 UTC | "{\"version\": \"5.0\", \"creation_date\": \"2005-11-16 15:48:42 UTC\", \"update_date\": \"2021-09-1(...TRUNCATED) |
HMDB0000016 | 5.0 | Deoxycorticosterone | [H][C@@]12CC[C@H](C(=O)CO)[C@@]1(C)CC[C@@]1([H])[C@@]2([H])CCC2=CC(=O)CC[C@]12C | "InChI=1S/C21H30O3/c1-20-9-7-14(23)11-13(20)3-4-15-16-5-6-18(19(24)12-22)21(16,2)10-8-17(15)20/h11,1(...TRUNCATED) | ZESRJSPZRDMNHY-YFWFAHHUSA-N | C21H30O3 | quantified | 2005-11-16 15:48:42 UTC | 2021-09-14 15:40:13 UTC | "{\"version\": \"5.0\", \"creation_date\": \"2005-11-16 15:48:42 UTC\", \"update_date\": \"2021-09-1(...TRUNCATED) |
HMDB frozen metadata
This is the 2021-10-13 HMDB 5.0 metadata snapshot, acquired from the documented frozen copy at https://zenodo.org/records/20747030 . It contains 217,920 metabolites and 1,104,876 non-2D spectral references. It is not a current HMDB snapshot or a spectrum/structure-pair collection.
The official HMDB website and export URLs returned HTTP 403 during acquisition. A publicly indexed alternate host had an expired TLS certificate. This fallback preserves available structure/provenance metadata; measured and predicted spectral archives remain pending official access. Spectral references do not contain chemical-shift lists or MS peaks. Their measurement type and nucleus remain unknown.
Original structure and identity fields, status, dates, and scientific metadata are retained in source_record_json. Article/database description prose is omitted from the public projection; the full source XML is retained locally with its checksum. XML formatting whitespace is stripped from leaf values. No molecule standardization, deduplication, chemistry, or benchmark filter is applied. 2D spectrum links are outside the processed reference view but remain in source record metadata. train is storage, not a benchmark split.
The source archive declares CC BY-NC 4.0 for non-commercial academic redistribution with attribution to HMDB. The source checksum is verified; source authorship and completeness beyond the frozen file have not been independently established. Cite HMDB and the frozen-source DOI.
Wishart et al., HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Research 50(D1), D622-D631. https://doi.org/10.1093/nar/gkab1062
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