MiMeDB: Showing metabocard for 2-Dehydro-3-deoxy-L-rhamnonate (MMDBc0031723)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:45:52 UTC

Update Date

2022-08-31 18:23:56 UTC

Metabolite ID

MMDBc0031723

Metabolite Identification

Common Name

2-Dehydro-3-deoxy-L-rhamnonate

Description

2-dehydro-3-deoxy-l-rhamnonate belongs to the class of Keto Fatty Acids. These are fatty acids containing a ketone group attached to the acyl chain.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 23-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4    5                                                       
CONECT    3    1    4    7   12                                             
CONECT    4    2    3    8   13                                             
CONECT    5    2    6    9                                                  
CONECT    6    5   10   11                                                  
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    3                                                            
CONECT   13    4                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
2-Dehydro-3,6-dideoxy-L-mannonate	ChEBI
2-Dehydro-3,6-dideoxy-L-mannonic acid	Generator
2-Dehydro-3-deoxy-L-rhamnonic acid	Generator
2-Dehydro-3-deoxy-L-rhamnonate	ChEBI

Molecular Formula

C₆H₁₀O₅

Average Mass

162.1406

Monoisotopic Mass

162.05282343

IUPAC Name

(4R,5S)-4,5-dihydroxy-2-oxohexanoic acid

Traditional Name

(4R,5S)-4,5-dihydroxy-2-oxohexanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10O5/c1-3(7)4(8)2-5(9)6(10)11/h3-4,7-8H,2H2,1H3,(H,10,11)/t3-,4+/m0/s1

InChI Key

FRIWJYNKZPJVRL-IUYQGCFVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Medium-chain keto acids and derivatives

Direct Parent

Medium-chain keto acids and derivatives

Alternative Parents

Substituents

Medium-chain keto acid
Alpha-keto acid
Beta-hydroxy ketone
Alpha-hydroxy ketone
1,2-diol
Secondary alcohol
Ketone
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Carbonyl group
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid (CHEBI:18078 )
hexonic acid (CHEBI:18078 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	119 g/L	ALOGPS
logP	-1.3	ALOGPS
logP	-0.73	ChemAxon
logS	-0.14	ALOGPS
pKa (Strongest Acidic)	3.06	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	34.77 m³·mol⁻¹	ChemAxon
Polarizability	14.59 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_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ot-2900000000-527c02e76a89144a4ebe	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-002k-9700000000-058bac2bc8bc9e2a411e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dj-9100000000-58ffe2f9b9affc7bb4e4	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-3900000000-d3497eb4995bd5913e87	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00dr-9300000000-2f7eaa4710b6f7eb62aa	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00dl-9100000000-13f3f80adf78936c1b31	2015-09-15	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	260.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	201.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	93.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	261.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	250.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	307.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	877.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	377.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	768.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	161.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	299.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	169.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	55.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	290.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	546.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	47.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	194.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	839.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	598.5

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_1	C[C@H](O[Si](C)(C)C)[C@H](O)CC(=O)C(=O)O	standard non polar	2025-10-24	1953.59
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_2	C[C@H](O)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	2197.31
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_3	C[C@H](O)[C@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1946.22
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_4	C[C@H](O)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1946.18
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_5	C[C@H](O[Si](C)(C)C)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	1704.38
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_6	C[C@H](O[Si](C)(C)C)[C@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1520.55
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_7	C[C@H](O[Si](C)(C)C)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	2278.16
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_8	C[C@H](O)[C@@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1871.4
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_9	C[C@H](O)[C@@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	1747.79
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_10	C[C@H](O)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1837.37
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_11	C[C@H](O[Si](C)(C)C)[C@@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2345.23
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_12	C[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	1847.43
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_13	C[C@H](O[Si](C)(C)C)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1643.59
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_14	C[C@H](O)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2399.9
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_15	C[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	910.997
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_1	C[C@H](O[Si](C)(C)C)[C@H](O)CC(=O)C(=O)O	standard polar	2025-10-24	1856.54
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_2	C[C@H](O)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	2202.69
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_3	C[C@H](O)[C@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1911.93
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_4	C[C@H](O)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	1854.49
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_5	C[C@H](O[Si](C)(C)C)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	1894.04
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_6	C[C@H](O[Si](C)(C)C)[C@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2061.93
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_7	C[C@H](O[Si](C)(C)C)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2167.24
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_8	C[C@H](O)[C@@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2207.79
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_9	C[C@H](O)[C@@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	1952.01
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_10	C[C@H](O)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2006.82
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_11	C[C@H](O[Si](C)(C)C)[C@@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2158.54
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_12	C[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	1970.47
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_13	C[C@H](O[Si](C)(C)C)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1919.0
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_14	C[C@H](O)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1498.12
Gas Chromatography	2-Dehydro-3-deoxy-L-rhamnonate_TMS_15	C[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2422.31

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
Bacteria/Eubacteria	Proteobacteria	46	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown
Archaea/Archaea	Crenarchaeota	1
Bacteria	Proteobacteria	3	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown
Bacteria/Eubacteria	Actinobacteria	1
Bacteria	Firmicutes	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

C03979

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6857359

PDB ID

Not Available

ChEBI ID

18078

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 2-Dehydro-3-deoxy-L-rhamnonate (MMDBc0031723)

MOL for #<Metabolite:0x00007f9a8defc250>

3D MOL for #<Metabolite:0x00007f9a8defc250>

3D SDF for #<Metabolite:0x00007f9a8defc250>

3D-SDF for #<Metabolite:0x00007f9a8defc250>

PDB for #<Metabolite:0x00007f9a8defc250>

3D PDB for #<Metabolite:0x00007f9a8defc250>

SMILES for #<Metabolite:0x00007f9a8defc250>

INCHI for #<Metabolite:0x00007f9a8defc250>

Structure for #<Metabolite:0x00007f9a8defc250>

3D Structure for #<Metabolite:0x00007f9a8defc250>