MiMeDB: Showing metabocard for L-Rhamnulose (MMDBc0029806)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:42:29 UTC

Update Date

2022-08-31 17:18:32 UTC

Metabolite ID

MMDBc0029806

Metabolite Identification

Common Name

L-Rhamnulose

Description

L-Rhamnulose is a breakdown product of L-rhamnose, which is ubiquitous and particularly abundant in some plants, such as buckthorn. Rhamnose is also one of the sugars regularly used to conduct the dual sugar permeability test. Rhamnose is fermented by some colonic bacteria into L-rhamnulose. Three bacterial (gut micrflora) enzymes are involved in Rhamnose degradation including rhaB (rhamulose kinase), rhaA (rhamnose isomerase), and rhaD (rhamnulose-1-phosphate aldolase). L-rhamnulose kinase catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose. E.coli are growing depending on L-rhamnose as a source of carbon and energy. (PMID: 40956 )

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
6-Deoxy-L-mannose	HMDB
6-Deoxy-L-sorbose	HMDB
6-Deoxy-L-xylo-hex-2-ulose	HMDB
L-Mannomethylose	HMDB
L-Rhamnose	HMDB
Rhamnulose	HMDB

Molecular Formula

C₆H₁₂O₅

Average Mass

164.1565

Monoisotopic Mass

164.068473494

IUPAC Name

(3S,4R,5S)-1,3,4,5-tetrahydroxyhexan-2-one

Traditional Name

L-rhamnulose

CAS Registry Number

14807-05-7

SMILES

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

InChI Identifier

InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h3,5-8,10-11H,2H2,1H3/t3-,5+,6+/m0/s1

InChI Key

QZNPNKJXABGCRC-OTWZMJIISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty alcohols

Direct Parent

Fatty alcohols

Alternative Parents

Substituents

Fatty alcohol
Acyloin
Beta-hydroxy ketone
Monosaccharide
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Polyol
Primary alcohol
Organooxygen compound
Organic oxygen compound
Carbonyl group
Alcohol
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	388 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.2	ChemAxon
logS	0.37	ALOGPS
pKa (Strongest Acidic)	10.47	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	36.02 m³·mol⁻¹	ChemAxon
Polarizability	15.42 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	splash10-0a4i-9100000000-ad22e0100103a9ec21f4	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-0550-7739500000-fc1eb1160f642aa0004e	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014j-2900000000-4fea56d8ac6e1f9c39f5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a6r-9200000000-1970754062af802fdcc1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-c31c6727c566e780cfc0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0k9i-9600000000-e099358e8071a9159c2f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0abi-9200000000-df6af27b57ded6f02536	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-70d5c6dd38db6d9ac9ab	2015-09-15	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

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007957	L-Rhamnose	L-Rhamnulose	Not Available	L-rhamnose isomerase	VMH	30371894
MMDBr0007958	Adenosine triphosphate	ADP	Not Available	Rhamnulokinase	VMH	30371894
MMDBr0013960	Adenosine triphosphate	ADP	Bifunctional enzyme RhaA/RhaB	Phosphorylation	RHEA	34755880
MMDBr0014298	Rhamnose	L-Rhamnulose	L-rhamnose isomerase	Isomerization	RHEA	34755880

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	104	Human feces; Human ; Human feces; pleural fluid plaque; bal; Human stool; Pig	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	20	Human feces; Human pleural fluid plaque; Human dental plaque; Human ; Human subgingival plaque; Human sputum; Human mucosa; Human supragingival plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	68	Human feces; Human stool; Human saliva; Human ; Human gastric fluid; Human urine	Metabolic reconstruction
Bacteria	Firmicutes	103	Human feces; Human ; Human pleural fluid plaque; Human stool; Catfish	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Planctomycetes	2	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Blood	Detected and Quantified	0.000437	0.000028			uM	Adult (>18 years old)	Not Specified	Normal	HMDB	18953024

External Links

HMDB ID

HMDB0010207

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB027362

KNApSAcK ID

Not Available

Chemspider ID

388459

KEGG Compound ID

C00861

BioCyc ID

RHAMNULOSE-1P

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439330

PDB ID

Not Available

ChEBI ID

17897

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 ]
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-Rhamnulose (MMDBc0029806)

MOL for #<Metabolite:0x000055d24aead068>

3D MOL for #<Metabolite:0x000055d24aead068>

3D SDF for #<Metabolite:0x000055d24aead068>

3D-SDF for #<Metabolite:0x000055d24aead068>

PDB for #<Metabolite:0x000055d24aead068>

3D PDB for #<Metabolite:0x000055d24aead068>

SMILES for #<Metabolite:0x000055d24aead068>

INCHI for #<Metabolite:0x000055d24aead068>

Structure for #<Metabolite:0x000055d24aead068>

3D Structure for #<Metabolite:0x000055d24aead068>