MiMeDB: Showing metabocard for L-rhamnono-1,4-lactone (MMDBc0054545)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:17:17 UTC

Update Date

2025-10-07 16:08:33 UTC

Metabolite ID

MMDBc0054545

Metabolite Identification

Common Name

L-rhamnono-1,4-lactone

Description

L-rhamnono-1,4-lactone is a lactone, specifically a cyclic ester derived from L-rhamnose, which plays a role in carbohydrate metabolism. Its chemical structure features a five-membered ring formed by the lactonization of the hydroxyl and carboxyl groups of L-rhamnose. In microbial metabolism, L-rhamnono-1,4-lactone is an important intermediate produced during the nonphosphorylative metabolic pathway, where L-rhamnose is oxidized by the enzyme L-rhamnose 1-dehydrogenase (RhaDH), utilizing NAD(P)+ as a cofactor (PMID:33482017 ). This metabolic process is crucial for certain microorganisms, including Escherichia coli, which actively catalyze the conversion of L-rhamnose to L-rhamnono-1,4-lactone (PMID:22481639 ). Additionally, the structural characterization of L-rhamnono-1,4-lactone has been achieved through single-crystal X-ray diffraction, providing insights into its molecular conformation and interactions (PMID:7805059 ). Overall, L-rhamnono-1,4-lactone serves as a significant compound in the biochemical pathways of various microorganisms, linking carbohydrate metabolism to energy production.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 05-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-15         0                                  
HETATM    1  C   UNK     0      23.676 -17.451   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      24.142 -18.920   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      24.905 -16.554   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      22.213 -16.971   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      25.682 -18.920   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      23.231 -20.157   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      26.162 -17.451   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      21.903 -15.466   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      21.069 -17.995   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      26.586 -20.164   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      27.618 -16.971   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0      23.368 -15.912   0.000  0.00  0.00           H+0
CONECT    1    2    3    4   12                                             
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2   10    7                                                  
CONECT    6    2                                                            
CONECT    7    3   11    5                                                  
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    7                                                            
CONECT   12    1                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
6-Deoxy-L-mannono-1,4-lactone	ChEBI
L-Rhamno-1,4-lactone	ChEBI

Molecular Formula

C₆H₁₀O₅

Average Mass

162.141

Monoisotopic Mass

162.052823422

IUPAC Name

(3R,4S,5S)-3,4-dihydroxy-5-[(1S)-1-hydroxyethyl]oxolan-2-one

Traditional Name

L-rhamnono-1,4-lactone

CAS Registry Number

Not Available

SMILES

[H][C@]1(OC(=O)[C@H](O)[C@@H]1O)[C@H](C)O

InChI Identifier

InChI=1S/C6H10O5/c1-2(7)5-3(8)4(9)6(10)11-5/h2-5,7-9H,1H3/t2-,3-,4+,5-/m0/s1

InChI Key

VASLEPDZAKCNJX-KLVWXMOXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Gamma butyrolactones

Direct Parent

Gamma butyrolactones

Alternative Parents

Substituents

Gamma butyrolactone
Tetrahydrofuran
Secondary alcohol
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

rhamnonolactone (CHEBI:17937 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	631 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-1.7	ChemAxon
logS	0.59	ALOGPS
pKa (Strongest Acidic)	11.63	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	33.24 m³·mol⁻¹	ChemAxon
Polarizability	14.58 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_3_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03dj-1900000000-4e32bd7fbd99d61773df	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01ot-2900000000-ae02aba11f2ddae5f53c	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4u-9000000000-3cf59a827e479277cc44	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-1900000000-c050309c0ae820228d62	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03dl-0900000000-6ac34f20a72ac27e9715	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-a6e522fcab5c4ad834fb	2019-02-23	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)	2025-10-24	327.4
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	174.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	105.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	278.1
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	276.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	342.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	876.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	518.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	917.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	197.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	284.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	188.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	47.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	280.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	627.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	69.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	238.7
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	927.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	651.3

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_1	C[C@H](O)[C@@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O	standard non polar	2025-10-24	1967.28
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_2	C[C@H](O)[C@@H]1OC(=O)[C@H](O)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1911.88
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_3	C[C@H](O[Si](C)(C)C)[C@@H]1OC(=O)[C@H](O)[C@@H]1O	standard non polar	2025-10-24	1689.43
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_4	C[C@H](O[Si](C)(C)C)[C@@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O	standard non polar	2025-10-24	2177.83
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_5	C[C@H](O)[C@@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1436.94
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_6	C[C@H](O[Si](C)(C)C)[C@@H]1OC(=O)[C@H](O)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1684.82
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_7	C[C@H](O[Si](C)(C)C)[C@@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1802.56
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_1	C[C@H](O)[C@@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O	standard polar	2025-10-24	2077.0
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_2	C[C@H](O)[C@@H]1OC(=O)[C@H](O)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	2555.26
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_3	C[C@H](O[Si](C)(C)C)[C@@H]1OC(=O)[C@H](O)[C@@H]1O	standard polar	2025-10-24	1756.78
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_4	C[C@H](O[Si](C)(C)C)[C@@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O	standard polar	2025-10-24	1857.34
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_5	C[C@H](O)[C@@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	1637.89
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_6	C[C@H](O[Si](C)(C)C)[C@@H]1OC(=O)[C@H](O)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	1658.78
Gas Chromatography	L-rhamnono-1,4-lactone_TMS_7	C[C@H](O[Si](C)(C)C)[C@@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	2092.43

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

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
Eukaryota/Fungi	Ascomycota	1
Archaea/Archaea	Euryarchaeota	1

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

Not Available

KEGG Compound ID

C02991

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

17937

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for L-rhamnono-1,4-lactone (MMDBc0054545)

MOL for #<Metabolite:0x00007f9af0a3e278>

3D MOL for #<Metabolite:0x00007f9af0a3e278>

3D SDF for #<Metabolite:0x00007f9af0a3e278>

3D-SDF for #<Metabolite:0x00007f9af0a3e278>

PDB for #<Metabolite:0x00007f9af0a3e278>

3D PDB for #<Metabolite:0x00007f9af0a3e278>

SMILES for #<Metabolite:0x00007f9af0a3e278>

INCHI for #<Metabolite:0x00007f9af0a3e278>

Structure for #<Metabolite:0x00007f9af0a3e278>

3D Structure for #<Metabolite:0x00007f9af0a3e278>