MiMeDB: Showing metabocard for 1-Deoxy-L-glycero-tetrulose 4-phosphate (MMDBc0031765)

Microbial

Plant

Animal

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:48:25 UTC

Update Date

2022-08-31 18:24:28 UTC

Metabolite ID

MMDBc0031765

Metabolite Identification

Common Name

1-Deoxy-L-glycero-tetrulose 4-phosphate

Description

1-deoxy-L-glycero-tetrulose 4-phosphate is an intermediate in the synthesis of riboflavin. It is a substrate for the enzyme 6,7-dimethyl-8-ribityllumazine synthase (RibE) which catalyzes the formation of 6,7-dimethyl-8 ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 1-deoxy-L-glycero-tetrulose 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Synonyms

Value	Source
3,4-Dihydroxy-2-butanone 4-phosphate	ChEBI
2-Hydroxy-3-oxobutyl phosphate	Kegg
3,4-Dihydroxy-2-butanone 4-phosphoric acid	Generator
2-Hydroxy-3-oxobutyl phosphoric acid	Generator
1-Deoxy-L-glycero-tetrulose 4-phosphoric acid	Generator
1-Deoxy-L-glycero-tetrulose 4-phosphate	ChEBI
L-3,4-Dihydroxybutan-2-one 4-phosphoric acid	Generator

Molecular Formula

C₄H₉O₆P

Average Mass

184.0844

Monoisotopic Mass

184.013674532

IUPAC Name

(2-hydroxy-3-oxobutoxy)phosphonic acid

Traditional Name

2-hydroxy-3-oxobutyl phosphate

CAS Registry Number

Not Available

SMILES

CC(=O)C(O)COP(O)(O)=O

InChI Identifier

InChI=1S/C4H9O6P/c1-3(5)4(6)2-10-11(7,8)9/h4,6H,2H2,1H3,(H2,7,8,9)

InChI Key

OKYHYXLCTGGOLM-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Monoalkyl phosphates

Alternative Parents

Substituents

Monoalkyl phosphate
Monosaccharide
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

oxoalkyl phosphate (CHEBI:50606 )
hydroxyalkyl phosphate (CHEBI:50606 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	24.9 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-1.3	ChemAxon
logS	-0.87	ALOGPS
pKa (Strongest Acidic)	1.39	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.06 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	34.81 m³·mol⁻¹	ChemAxon
Polarizability	14.38 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 (Non-derivatized) - 70eV, Positive	splash10-0007-9400000000-971962d1d681055c1e3c	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-3900000000-a3d7948fc05904e06862	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014s-9500000000-31ec6e7cea40d06a6892	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-014r-9000000000-beb8708b4dc7d349cdea	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-003r-5900000000-9e4612499bf4e2f07fc5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-425643565aa835d01981	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-0ef89293cd43e0a1a071	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-9000000000-676cc37240e7d973e2af	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9000000000-a6ca687b980625713d4b	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001l-9000000000-c6888871a1308dc01b19	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002b-9000000000-e30f5f83dc1e6cb4f00f	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-10-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	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	540.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	424.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	41.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	219.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	291.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	330.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	450.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	758.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	940.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	191.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	424.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	202.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	35.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	521.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	730.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	73.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	321.1
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	711.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	616.5

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_1	CC(=O)C(COP(=O)(O)O)O[Si](C)(C)C	standard non polar	2025-10-24	1971.3
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_2	CC(=O)C(O)COP(=O)(O)O[Si](C)(C)C	standard non polar	2025-10-24	1628.59
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_3	CC(O[Si](C)(C)C)=C(O)COP(=O)(O)O	standard non polar	2025-10-24	2027.92
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_4	C=C(O[Si](C)(C)C)C(O)COP(=O)(O)O	standard non polar	2025-10-24	1948.77
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_5	CC(=O)C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2365.83
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_6	CC(O[Si](C)(C)C)=C(COP(=O)(O)O)O[Si](C)(C)C	standard non polar	2025-10-24	1524.95
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_7	C=C(O[Si](C)(C)C)C(COP(=O)(O)O)O[Si](C)(C)C	standard non polar	2025-10-24	2083.88
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_8	CC(=O)C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1699.05
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_9	CC(O[Si](C)(C)C)=C(O)COP(=O)(O)O[Si](C)(C)C	standard non polar	2025-10-24	1874.67
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_10	C=C(O[Si](C)(C)C)C(O)COP(=O)(O)O[Si](C)(C)C	standard non polar	2025-10-24	1762.27
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_11	CC(=O)C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2309.75
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_12	CC(O[Si](C)(C)C)=C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2346.69
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_13	C=C(O[Si](C)(C)C)C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2172.0
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_14	CC(O[Si](C)(C)C)=C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1658.22
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_15	C=C(O[Si](C)(C)C)C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2221.66
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_16	CC(O[Si](C)(C)C)=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2480.5
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_17	C=C(O[Si](C)(C)C)C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1818.16
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_1	CC(=O)C(COP(=O)(O)O)O[Si](C)(C)C	standard polar	2025-10-24	2221.14
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_2	CC(=O)C(O)COP(=O)(O)O[Si](C)(C)C	standard polar	2025-10-24	2133.58
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_3	CC(O[Si](C)(C)C)=C(O)COP(=O)(O)O	standard polar	2025-10-24	2381.55
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_4	C=C(O[Si](C)(C)C)C(O)COP(=O)(O)O	standard polar	2025-10-24	2038.09
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_5	CC(=O)C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1854.72
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_6	CC(O[Si](C)(C)C)=C(COP(=O)(O)O)O[Si](C)(C)C	standard polar	2025-10-24	1971.18
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_7	C=C(O[Si](C)(C)C)C(COP(=O)(O)O)O[Si](C)(C)C	standard polar	2025-10-24	2124.02
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_8	CC(=O)C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2289.69
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_9	CC(O[Si](C)(C)C)=C(O)COP(=O)(O)O[Si](C)(C)C	standard polar	2025-10-24	2491.22
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_10	C=C(O[Si](C)(C)C)C(O)COP(=O)(O)O[Si](C)(C)C	standard polar	2025-10-24	1928.06
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_11	CC(=O)C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1818.43
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_12	CC(O[Si](C)(C)C)=C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2132.96
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_13	C=C(O[Si](C)(C)C)C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1997.31
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_14	CC(O[Si](C)(C)C)=C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2977.2
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_15	C=C(O[Si](C)(C)C)C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1970.25
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_16	CC(O[Si](C)(C)C)=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2404.36
Gas Chromatography	1-Deoxy-L-glycero-tetrulose 4-phosphate_TMS_17	C=C(O[Si](C)(C)C)C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2174.83

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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
Flavin 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
MMDBr0019052	5-Amino-6-ribitylamino uracil	6,7-Dimethyl-8-(1-D-ribityl)lumazine	Riboflavin synthase	Synthesis	PathBank	31602464
MMDBr0019054	D-Ribulose 5-phosphate	Formic acid	3,4-dihydroxy-2-butanone 4-phosphate synthase	Synthesis	PathBank	31602464
MMDBr0019646	D-Ribulose 5-phosphate	Formic acid	3,4-dihydroxy-2-butanone 4-phosphate synthase	Synthesis	PathBank	31602464
MMDBr0019647	5-Amino-6-ribitylamino uracil	6,7-Dimethyl-8-(1-D-ribityl)lumazine	6,7-dimethyl-8-ribityllumazine synthase	Synthesis	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/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

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

External Links

HMDB ID

HMDB0304013

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030244

KNApSAcK ID

Not Available

Chemspider ID

649

KEGG Compound ID

C15556

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

50606

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

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 1-Deoxy-L-glycero-tetrulose 4-phosphate (MMDBc0031765)

MOL for #<Metabolite:0x00007f9ac477ea50>

3D MOL for #<Metabolite:0x00007f9ac477ea50>

3D SDF for #<Metabolite:0x00007f9ac477ea50>

3D-SDF for #<Metabolite:0x00007f9ac477ea50>

PDB for #<Metabolite:0x00007f9ac477ea50>

3D PDB for #<Metabolite:0x00007f9ac477ea50>

SMILES for #<Metabolite:0x00007f9ac477ea50>

INCHI for #<Metabolite:0x00007f9ac477ea50>

Structure for #<Metabolite:0x00007f9ac477ea50>

3D Structure for #<Metabolite:0x00007f9ac477ea50>