MiMeDB: Showing metabocard for 4,5-Dihydroxy-2,3-pentanedione (MMDBc0030185)

Microbial

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:57:28 UTC

Update Date

2022-08-31 17:40:31 UTC

Metabolite ID

MMDBc0030185

Metabolite Identification

Common Name

4,5-Dihydroxy-2,3-pentanedione

Description

4,5-dihydroxy-2,3-pentanedione is a member of the chemical class known as Beta Ketoaldehydes. These are organic compounds containing an aldehyde substituted with a keto group on the second carbon atom. Dihydropyrimidine dehydrogenase (DPD) is the initial and rate-limiting enzyme in the catabolism of 5-FU. (PMID 9865912 ) E. coli expression system is a valuable tool for examining DPD enzymatic variants. (PMID 9439663 )

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₅H₈O₄

Average Mass

132.1146

Monoisotopic Mass

132.042258744

IUPAC Name

(4R)-4,5-dihydroxypentane-2,3-dione

Traditional Name

(4R)-4,5-dihydroxypentane-2,3-dione

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)C(=O)C(C)=O

InChI Identifier

InChI=1S/C5H8O4/c1-3(7)5(9)4(8)2-6/h4,6,8H,2H2,1H3/t4-/m1/s1

InChI Key

UYTRITJAZOPLCZ-SCSAIBSYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharides

Alternative Parents

Substituents

Monosaccharide
Beta-hydroxy ketone
Alpha-diketone
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Ketone
1,2-diol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	272 g/L	ALOGPS
logP	-0.95	ALOGPS
logP	-0.9	ChemAxon
logS	0.31	ALOGPS
pKa (Strongest Acidic)	11.69	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	29.28 m³·mol⁻¹	ChemAxon
Polarizability	11.94 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00lr-3900000000-6d2a245dcbab05272fc6	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03xr-9300000000-3bb219976347e8bbd517	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0btc-9000000000-5a2f0227afbabb99311f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0089-9700000000-87c806aa0eef96279ffa	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-05g0-9200000000-2d86733dc438d3ffd1e1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-c0f0a293355274672fab	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	176.3
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	100.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	115.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	280.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	263.3
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	335.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	920.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	226.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	739.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	199.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	275.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	198.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	64.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	213.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	583.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	51.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	238.5
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	890.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	612.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_1	CC(=O)C(=O)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	1685.51
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_2	CC(=O)C(=O)[C@H](O)CO[Si](C)(C)C	standard non polar	2025-10-24	1592.19
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_3	CC(=O)C(O[Si](C)(C)C)=C(O)CO	standard non polar	2025-10-24	2385.39
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_4	C=C(O[Si](C)(C)C)C(=O)[C@H](O)CO	standard non polar	2025-10-24	2129.28
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_5	CC(=O)C(=O)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1537.37
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_6	CC(=O)C(O[Si](C)(C)C)=C(CO)O[Si](C)(C)C	standard non polar	2025-10-24	1537.35
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_7	C=C(O[Si](C)(C)C)C(=O)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	1127.82
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_8	CC(=O)C(O[Si](C)(C)C)=C(O)CO[Si](C)(C)C	standard non polar	2025-10-24	2172.73
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_9	C=C(O[Si](C)(C)C)C(=O)[C@H](O)CO[Si](C)(C)C	standard non polar	2025-10-24	2429.52
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_10	C=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(O)CO	standard non polar	2025-10-24	2461.95
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_11	CC(=O)C(O[Si](C)(C)C)=C(CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1912.41
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_12	C=C(O[Si](C)(C)C)C(=O)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1772.14
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_13	C=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(CO)O[Si](C)(C)C	standard non polar	2025-10-24	2448.37
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_14	C=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(O)CO[Si](C)(C)C	standard non polar	2025-10-24	1973.32
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_15	C=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1375.34
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_1	CC(=O)C(=O)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	2025.16
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_2	CC(=O)C(=O)[C@H](O)CO[Si](C)(C)C	standard polar	2025-10-24	2140.09
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_3	CC(=O)C(O[Si](C)(C)C)=C(O)CO	standard polar	2025-10-24	2181.08
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_4	C=C(O[Si](C)(C)C)C(=O)[C@H](O)CO	standard polar	2025-10-24	1985.75
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_5	CC(=O)C(=O)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1772.1
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_6	CC(=O)C(O[Si](C)(C)C)=C(CO)O[Si](C)(C)C	standard polar	2025-10-24	1661.25
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_7	C=C(O[Si](C)(C)C)C(=O)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	2707.32
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_8	CC(=O)C(O[Si](C)(C)C)=C(O)CO[Si](C)(C)C	standard polar	2025-10-24	2035.53
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_9	C=C(O[Si](C)(C)C)C(=O)[C@H](O)CO[Si](C)(C)C	standard polar	2025-10-24	2400.61
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_10	C=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(O)CO	standard polar	2025-10-24	1891.63
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_11	CC(=O)C(O[Si](C)(C)C)=C(CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2100.39
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_12	C=C(O[Si](C)(C)C)C(=O)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1900.93
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_13	C=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(CO)O[Si](C)(C)C	standard polar	2025-10-24	2153.07
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_14	C=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(O)CO[Si](C)(C)C	standard polar	2025-10-24	2531.0
Gas Chromatography	4,5-Dihydroxy-2,3-pentanedione_TMS_15	C=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1756.28

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Name	SMPDB/PathBank	Species
Quorum sensing - Autoinducer-2 Biosynthesis

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019197	S-ribosyl-L-homocysteine	4,5-Dihydroxy-2,3-pentanedione	S-ribosylhomocysteine lyase	Non-hydrolytic bond cleavage (or its reversal)	PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	347	Human feces; Human pleural fluid plaque; Pig ; Human ; Human subgingival plaque; Cattle ; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	160	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	113	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	83	Human feces; Human appendix biopsy; Human ; Human gastric fluid; Human urine; Human saliva; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	10	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	3		Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	2	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

4,5-Dihydroxy-2,3-pentanedione

METLIN ID

Not Available

PubChem Compound

25200942

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for 4,5-Dihydroxy-2,3-pentanedione (MMDBc0030185)

MOL for #<Metabolite:0x00007f9aa2121f08>

3D MOL for #<Metabolite:0x00007f9aa2121f08>

3D SDF for #<Metabolite:0x00007f9aa2121f08>

3D-SDF for #<Metabolite:0x00007f9aa2121f08>

PDB for #<Metabolite:0x00007f9aa2121f08>

3D PDB for #<Metabolite:0x00007f9aa2121f08>

SMILES for #<Metabolite:0x00007f9aa2121f08>

INCHI for #<Metabolite:0x00007f9aa2121f08>

Structure for #<Metabolite:0x00007f9aa2121f08>

3D Structure for #<Metabolite:0x00007f9aa2121f08>