MiMeDB: Showing metabocard for L-Lyxopyranose (MMDBc0000295)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2020-10-28 00:08:58 UTC

Update Date

2025-10-07 16:04:21 UTC

Metabolite ID

MMDBc0000295

Metabolite Identification

Common Name

L-Lyxopyranose

Description

L-Lyxopyranose is a carbohydrate belonging to the class of aldoses, specifically a hexose sugar. Its chemical structure features a six-membered pyranose ring with hydroxyl groups attached at various positions, which plays a crucial role in its reactivity and interactions. In synthetic organic chemistry, L-Lyxopyranose serves as a valuable building block; for instance, it can undergo chemical transformations such as the introduction of substituents at the C-4 position, as demonstrated in the treatment of 2,3-O-isopropylidene-1-O-methyl-4-O-phenoxythiocarbonyl-alpha-l-lyxopyranose with beta-tributylstannyl styrene (PMID:15202900 ). Additionally, L-Lyxopyranose is involved in the synthesis of nucleosides, contributing to the formation of pyrimidine and purine nucleosides, which are essential components of nucleic acids (PMID:1177062 ). These pathways highlight the compound's significance in both synthetic and biological contexts, showcasing its versatility in various chemical reactions and its role in the biosynthesis of critical biomolecules.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
L-Lyxose	ChEBI
WURCS=2.0/1,1,0/[a221h-1x_1-5]/1/	ChEBI

Molecular Formula

C₅H₁₀O₅

Average Mass

150.13

Monoisotopic Mass

150.052823422

IUPAC Name

(3R,4R,5S)-oxane-2,3,4,5-tetrol

Traditional Name

L-lyxopyranose

CAS Registry Number

1949-78-6

SMILES

O[C@H]1COC(O)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4+,5?/m0/s1

InChI Key

SRBFZHDQGSBBOR-AEQNFAKKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

L-lyxose (CHEBI:62321 )
Aldoses (C01508 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1220 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-2.3	ChemAxon
logS	0.91	ALOGPS
pKa (Strongest Acidic)	11.31	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	29.96 m³·mol⁻¹	ChemAxon
Polarizability	13.28 Å³	ChemAxon
Number of Rings	1	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	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	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	434.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	290.1
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	40.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	222.0
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	286.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	321.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	619.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	682.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	786.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	178.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	355.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	194.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	38.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	309.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	652.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	75.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	260.1
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	742.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	583.4

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	L-Lyxopyranose_TMS_1	C[Si](C)(C)O[C@H]1COC(O)[C@H](O)[C@@H]1O	standard non polar	2025-10-23	1683.97
Gas Chromatography	L-Lyxopyranose_TMS_2	C[Si](C)(C)OC1OC[C@H](O)[C@@H](O)[C@H]1O	standard non polar	2025-10-23	1831.63
Gas Chromatography	L-Lyxopyranose_TMS_3	C[Si](C)(C)O[C@H]1C(O)OC[C@H](O)[C@H]1O	standard non polar	2025-10-23	1809.01
Gas Chromatography	L-Lyxopyranose_TMS_4	C[Si](C)(C)O[C@@H]1[C@@H](O)COC(O)[C@@H]1O	standard non polar	2025-10-23	1589.57
Gas Chromatography	L-Lyxopyranose_TMS_5	C[Si](C)(C)OC1OC[C@H](O[Si](C)(C)C)[C@@H](O)[C@H]1O	standard non polar	2025-10-23	1905.77
Gas Chromatography	L-Lyxopyranose_TMS_6	C[Si](C)(C)O[C@H]1COC(O)[C@H](O[Si](C)(C)C)[C@@H]1O	standard non polar	2025-10-23	1417.35
Gas Chromatography	L-Lyxopyranose_TMS_7	C[Si](C)(C)O[C@H]1COC(O)[C@H](O)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-23	1953.92
Gas Chromatography	L-Lyxopyranose_TMS_8	C[Si](C)(C)OC1OC[C@H](O)[C@@H](O[Si](C)(C)C)[C@H]1O	standard non polar	2025-10-23	1857.51
Gas Chromatography	L-Lyxopyranose_TMS_9	C[Si](C)(C)OC1OC[C@H](O)[C@@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-23	2191.42
Gas Chromatography	L-Lyxopyranose_TMS_10	C[Si](C)(C)O[C@H]1C(O)OC[C@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-23	2124.3
Gas Chromatography	L-Lyxopyranose_TMS_11	C[Si](C)(C)OC1OC[C@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O	standard non polar	2025-10-23	2023.3
Gas Chromatography	L-Lyxopyranose_TMS_12	C[Si](C)(C)OC1OC[C@H](O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-23	1806.18
Gas Chromatography	L-Lyxopyranose_TMS_13	C[Si](C)(C)O[C@H]1COC(O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-23	2305.8
Gas Chromatography	L-Lyxopyranose_TMS_14	C[Si](C)(C)OC1OC[C@H](O)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-23	1393.65
Gas Chromatography	L-Lyxopyranose_TMS_15	C[Si](C)(C)OC1OC[C@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-23	1848.07
Gas Chromatography	L-Lyxopyranose_TMS_1	C[Si](C)(C)O[C@H]1COC(O)[C@H](O)[C@@H]1O	standard polar	2025-10-23	1901.84
Gas Chromatography	L-Lyxopyranose_TMS_2	C[Si](C)(C)OC1OC[C@H](O)[C@@H](O)[C@H]1O	standard polar	2025-10-23	2025.25
Gas Chromatography	L-Lyxopyranose_TMS_3	C[Si](C)(C)O[C@H]1C(O)OC[C@H](O)[C@H]1O	standard polar	2025-10-23	1950.98
Gas Chromatography	L-Lyxopyranose_TMS_4	C[Si](C)(C)O[C@@H]1[C@@H](O)COC(O)[C@@H]1O	standard polar	2025-10-23	2268.07
Gas Chromatography	L-Lyxopyranose_TMS_5	C[Si](C)(C)OC1OC[C@H](O[Si](C)(C)C)[C@@H](O)[C@H]1O	standard polar	2025-10-23	2159.39
Gas Chromatography	L-Lyxopyranose_TMS_6	C[Si](C)(C)O[C@H]1COC(O)[C@H](O[Si](C)(C)C)[C@@H]1O	standard polar	2025-10-23	1881.11
Gas Chromatography	L-Lyxopyranose_TMS_7	C[Si](C)(C)O[C@H]1COC(O)[C@H](O)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-23	2093.17
Gas Chromatography	L-Lyxopyranose_TMS_8	C[Si](C)(C)OC1OC[C@H](O)[C@@H](O[Si](C)(C)C)[C@H]1O	standard polar	2025-10-23	2471.13
Gas Chromatography	L-Lyxopyranose_TMS_9	C[Si](C)(C)OC1OC[C@H](O)[C@@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-23	1610.56
Gas Chromatography	L-Lyxopyranose_TMS_10	C[Si](C)(C)O[C@H]1C(O)OC[C@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-23	2188.67
Gas Chromatography	L-Lyxopyranose_TMS_11	C[Si](C)(C)OC1OC[C@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O	standard polar	2025-10-23	3365.4
Gas Chromatography	L-Lyxopyranose_TMS_12	C[Si](C)(C)OC1OC[C@H](O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-23	2412.99
Gas Chromatography	L-Lyxopyranose_TMS_13	C[Si](C)(C)O[C@H]1COC(O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-23	2367.48
Gas Chromatography	L-Lyxopyranose_TMS_14	C[Si](C)(C)OC1OC[C@H](O)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-23	2094.08
Gas Chromatography	L-Lyxopyranose_TMS_15	C[Si](C)(C)OC1OC[C@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-23	2103.68

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

Not Available

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
MMDBr0019366	L-Lyxopyranose	L-Xylulose	L-rhamnose isomerase	Isomerization	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

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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

388605

KEGG Compound ID

C01508

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Lyxose

METLIN ID

Not Available

PubChem Compound

439508

PDB ID

Not Available

ChEBI ID

62321

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 L-Lyxopyranose (MMDBc0000295)

MOL for #<Metabolite:0x00007f9adbc6cfc8>

3D MOL for #<Metabolite:0x00007f9adbc6cfc8>

3D SDF for #<Metabolite:0x00007f9adbc6cfc8>

3D-SDF for #<Metabolite:0x00007f9adbc6cfc8>

PDB for #<Metabolite:0x00007f9adbc6cfc8>

3D PDB for #<Metabolite:0x00007f9adbc6cfc8>

SMILES for #<Metabolite:0x00007f9adbc6cfc8>

INCHI for #<Metabolite:0x00007f9adbc6cfc8>

Structure for #<Metabolite:0x00007f9adbc6cfc8>

3D Structure for #<Metabolite:0x00007f9adbc6cfc8>