MiMeDB: Showing metabocard for Rhamnose (MMDBc0000158)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:37:59 UTC

Update Date

2024-04-30 19:31:15 UTC

Metabolite ID

MMDBc0000158

Metabolite Identification

Common Name

Rhamnose

Description

Rhamnose (Rham) is a naturally occurring deoxy sugar. It can be classified as either a methyl-pentose or a 6-deoxy-hexose. Rhamnose occurs in nature in its L-form as L-rhamnose (6-deoxy-L-mannose). This is unusual, since most of the naturally occurring sugars are in D-form. Rhamnose is commonly bound to other sugars in nature. It is a common glycone component of glycosides from many plants. Rhamnose is also a component of the outer cell membrane of certain bacteria. L-rhamnose is metabolized to L-Lactaldehyde, which is a branching point in the metabolic pathway of L-fucose and L-rhamnose utilization. It exists in two anomeric forms, alpha-L-rhamnose and beta-L-rhamnose. Rhamnose has been found in Klebsiella, Pseudomonas (https://link.springer.com/article/10.1007/BF00369505) (https://onlinelibrary.wiley.com/doi/abs/10.1002/ejlt.200300816).

Structure

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

Synonyms

Value	Source
6-Deoxy-L-mannose	ChEBI
L-(+)-Rhamnose	ChEBI
L-Mannomethylose	ChEBI
L-Rha	ChEBI
L-Rhamnose	ChEBI
L-Rhamnopyranose	Kegg
6-Deoxy-L(+)-mannose	HMDB
6-Deoxy-L-mannopyranose	HMDB
6-Deoxy-mannose	HMDB
6-Deoxyhexopyranose	HMDB
6-Deoxyhexose	HMDB
6-Deoxymannose	HMDB
Isodulcit	HMDB
Isodulcitol	HMDB
L(+)-Rhamnose	HMDB
L(+)-Rhamnose monohydrate	HMDB
L-(+)-Rhamnose 1-hydrate	HMDB
L-(+)-Rhamnose hydrate = 6-deoxy-L-mannose monohydrate	HMDB
L-(+)-Rhamnose monohydrate	HMDB
L-Rhamnose for biochemistry	HMDB
L-Rhamnose monohydrate	HMDB
Locaose	HMDB
mono(6-Deoxy-b-L-mannopyranosyl) ester	HMDB
mono(6-Deoxy-beta-L-mannopyranosyl) ester	HMDB
p-(6-Deoxy-b-L-mannopyranosyl) ester	HMDB
p-(6-Deoxy-beta-L-mannopyranosyl) ester	HMDB
Rhamnopyranose	HMDB
Rhamnosemonohydrate	HMDB
UDP-Rhamnose	HMDB
Uridine 5-pyrophosphate	HMDB
Uridine diphosphate rhamnose	HMDB
Deoxymannose	HMDB
Rhamnose, L isomer	HMDB
Rhamnose, L-isomer	HMDB
Rhamnose	MeSH, HMDB

Molecular Formula

C₆H₁₂O₅

Average Mass

164.1565

Monoisotopic Mass

164.068473494

IUPAC Name

(3R,4R,5R,6S)-6-methyloxane-2,3,4,5-tetrol

Traditional Name

L-(+)-rhamnose

CAS Registry Number

3615-41-6

SMILES

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

InChI Identifier

InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6?/m0/s1

InChI Key

SHZGCJCMOBCMKK-JFNONXLTSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Hexoses

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

L-rhamnose (CHEBI:62346 )
Deoxy sugars (C00507 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	827 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-1.9	ChemAxon
logS	0.7	ALOGPS
pKa (Strongest Acidic)	11.3	ChemAxon
pKa (Strongest Basic)	-3.6	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	34.38 m³·mol⁻¹	ChemAxon
Polarizability	15.36 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
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014i-0900000000-ff79aee2e9ac3a4f53c8	2018-05-25	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014i-0900000000-23d1bd654495aefbf615	2018-05-25	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014i-0900000000-ff79aee2e9ac3a4f53c8	2018-05-25	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014i-0900000000-23d1bd654495aefbf615	2018-05-25	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4j-9500000000-cfa9e0d8f1f20b29e5d8	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-002r-9346400000-7524daf3b04caf0c441a	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-06	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0019-9600000000-8cb337afbc2d297157bf	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0uy0-9600000000-cb7dbb4d86a5bc544704	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-014i-9200000000-89022407246ea7a22497	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-03di-0900000000-2196b54a850c456b7ee8	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-03di-0900000000-2196b54a850c456b7ee8	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0002-3900000000-fa9bb45e13786471d8fc	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0900-4900000000-b5658046687bc01ef47f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0a6r-9300000000-e3c74a1e2b1ad285c324	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0900000000-5daf054ff3eb9127d3ca	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014j-0900000000-f7729c93b964e01cb774	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a70-9000000000-2c46a67befe14c31d7a9	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-2900000000-86321b083a11f93bb55b	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03dj-5900000000-2accd457fe7b58b9b032	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-9e349c8fad042f6a3e99	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-016s-0900000000-1b35b25727b809781557	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9400000000-d296c72cacbcd6d61db1	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4j-9000000000-daa4eb13673f38090d73	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-2900000000-39b12ef61b5dc955b65a	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052f-9200000000-b035b501120515e5ba70	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-b4e3f8e66eccd71547b0	2021-09-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces
Platelet

Tissue Locations

Platelet

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

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	Firmicutes	51	Human ; Human feces; Human stool; Human urine; Human saliva; Human subgingival plaque; Catfish	Microbial culture
Bacteria	Bacteroidetes	26	Human saliva; Human stool; Human feces; Human urine; Human ; Human gastric fluid; Human subgingival plaque	Microbial culture
Bacteria	Actinobacteria	2	Human feces; Human stool; Human	Microbial culture
Bacteria	Proteobacteria	61	Human ; Human feces	Microbial culture
Bacteria	Deinococcus-thermus	1		Microbial culture
Bacteria	Planctomycetes	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified	Infant (0-1 year old)	Both	Normal	HMDB	22411374
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Colorectal cancer	HMDB	25037050
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Colorectal cancer	HMDB	27015276
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	HMDB	27275383
Human Platelet	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Infant (0-1 year old)	Both	Normal	HMDB	22411374
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	25037050

External Links

HMDB ID

HMDB0000849

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Rhamnose

METLIN ID

5812

PubChem Compound

25310

PDB ID

Not Available

ChEBI ID

62346

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bjarnason I, Smethurst P, Macpherson A, Walker F, McElnay JC, Passmore AP, Menzies IS: Glucose and citrate reduce the permeability changes caused by indomethacin in humans. Gastroenterology. 1992 May;102(5):1546-50. doi: 10.1016/0016-5085(92)91712-d. [PubMed:1568563 ]
Citron DM, Baron EJ, Finegold SM, Goldstein EJ: Short prereduced anaerobically sterilized (PRAS) biochemical scheme for identification of clinical isolates of bile-resistant Bacteroides species. J Clin Microbiol. 1990 Oct;28(10):2220-3. doi: 10.1128/jcm.28.10.2220-2223.1990. [PubMed:2229345 ]
Whaley DN, Wiggs LS, Miller PH, Srivastava PU, Miller JM: Use of Presumpto Plates to identify anaerobic bacteria. J Clin Microbiol. 1995 May;33(5):1196-202. doi: 10.1128/jcm.33.5.1196-1202.1995. [PubMed:7615728 ]
Ohri SK, Somasundaram S, Koak Y, Macpherson A, Keogh BE, Taylor KM, Menzies IS, Bjarnason I: The effect of intestinal hypoperfusion on intestinal absorption and permeability during cardiopulmonary bypass. Gastroenterology. 1994 Feb;106(2):318-23. doi: 10.1016/0016-5085(94)90588-6. [PubMed:8299899 ]
Miki K, Butler R, Moore D, Davidson G: Rapid and simultaneous quantification of rhamnose, mannitol, and lactulose in urine by HPLC for estimating intestinal permeability in pediatric practice. Clin Chem. 1996 Jan;42(1):71-5. [PubMed:8565237 ]
Van Kuilenburg AB, Van Lenthe H, Assmann B, Gohlich-Ratmann G, Hoffmann GF, Brautigam C, Wevers RA, Van Gennip AH: Detection of beta-ureidopropionase deficiency with HPLC-electrospray tandem mass spectrometry and confirmation of the defect at the enzyme level. J Inherit Metab Dis. 2001 Dec;24(7):725-32. doi: 10.1023/a:1012997406132. [PubMed:11804209 ]
Ohse M, Matsuo M, Ishida A, Kuhara T: Screening and diagnosis of beta-ureidopropionase deficiency by gas chromatographic/mass spectrometric analysis of urine. J Mass Spectrom. 2002 Sep;37(9):954-62. doi: 10.1002/jms.354. [PubMed:12271438 ]
Chia JS, Lin YL, Lien HT, Chen JY: Platelet aggregation induced by serotype polysaccharides from Streptococcus mutans. Infect Immun. 2004 May;72(5):2605-17. doi: 10.1128/IAI.72.5.2605-2617.2004. [PubMed:15102769 ]
Albers MJ, Steyerberg EW, Hazebroek FW, Mourik M, Borsboom GJ, Rietveld T, Huijmans JG, Tibboel D: Glutamine supplementation of parenteral nutrition does not improve intestinal permeability, nitrogen balance, or outcome in newborns and infants undergoing digestive-tract surgery: results from a double-blind, randomized, controlled trial. Ann Surg. 2005 Apr;241(4):599-606. doi: 10.1097/01.sla.0000157270.24991.71. [PubMed:15798461 ]
Frirdich E, Whitfield C: Lipopolysaccharide inner core oligosaccharide structure and outer membrane stability in human pathogens belonging to the Enterobacteriaceae. J Endotoxin Res. 2005;11(3):133-44. doi: 10.1179/096805105X46592. [PubMed:15949142 ]
Anderson AD, Poon P, Greenway GM, MacFie J: A simple method for the analysis of urinary sucralose for use in tests of intestinal permeability. Ann Clin Biochem. 2005 May;42(Pt 3):224-6. doi: 10.1258/0004563053857923. [PubMed:15949159 ]
Nomura R, Nakano K, Ooshima T: Molecular analysis of the genes involved in the biosynthesis of serotype specific polysaccharide in the novel serotype k strains of Streptococcus mutans. Oral Microbiol Immunol. 2005 Oct;20(5):303-9. doi: 10.1111/j.1399-302X.2005.00231.x. [PubMed:16101966 ]
Hosono M, Sugawara S, Ogawa Y, Kohno T, Takayanagi M, Nitta K: Purification, characterization, cDNA cloning, and expression of asialofetuin-binding C-type lectin from eggs of shishamo smelt (Osmerus [Spirinchus] lanceolatus). Biochim Biophys Acta. 2005 Sep 15;1725(2):160-73. doi: 10.1016/j.bbagen.2005.07.009. [PubMed:16112459 ]

Showing metabocard for Rhamnose (MMDBc0000158)

MOL for #<Metabolite:0x00007fecb262ccc0>

3D MOL for #<Metabolite:0x00007fecb262ccc0>

3D SDF for #<Metabolite:0x00007fecb262ccc0>

3D-SDF for #<Metabolite:0x00007fecb262ccc0>

PDB for #<Metabolite:0x00007fecb262ccc0>

3D PDB for #<Metabolite:0x00007fecb262ccc0>

SMILES for #<Metabolite:0x00007fecb262ccc0>

INCHI for #<Metabolite:0x00007fecb262ccc0>

Structure for #<Metabolite:0x00007fecb262ccc0>

3D Structure for #<Metabolite:0x00007fecb262ccc0>