MiMeDB: Showing metabocard for Ribitol (MMDBc0000110)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:36:15 UTC

Update Date

2024-10-11 03:19:17 UTC

Metabolite ID

MMDBc0000110

Metabolite Identification

Common Name

Ribitol

Description

Ribitol is a metabolic end product formed by the reduction of ribose in human fibroblasts and erythrocytes (pentitol, sugar alcohol, polyol). Export of ribitol across the cell membrane indicates that can be cleared from the body without metabolic conversion (PMID 15234337 ). Several inborn errors of metabolism with abnormal polyol concentrations in body fluids are known to date, such as ribose-5-phosphate isomerase deficiency. Most of these defects can be diagnosed by the assessment of urinary concentrations of polyols (PMID 16435188 ). Ribitol is normally absent in Breast milk (PMID 16456418 ).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2R,3S,4S)-Pentane-1,2,3,4,5-pentol	ChEBI
Adonitol	ChEBI
D-Adonitol	ChEBI
D-Ribitol	ChEBI
L-Ribitol	ChEBI
1,2,3,4,5-Pentanepentol	HMDB
Adonit	HMDB
Adonite	HMDB
Pentitol	HMDB

Molecular Formula

C₅H₁₂O₅

Average Mass

152.1458

Monoisotopic Mass

152.068473494

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

488-81-3

SMILES

Not Available

InChI Identifier

InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5-

InChI Key

HEBKCHPVOIAQTA-ZXFHETKHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar alcohols

Alternative Parents

Substituents

Sugar alcohol
Monosaccharide
Secondary alcohol
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribitol (CHEBI:15963 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Not Available

Spectra

Not Available

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Placenta
Prostate
Urine

Tissue Locations

Placenta
Prostate

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
MMDBr0002721	D-Ribose	Ribitol	Not Available		VMH	15234337
MMDBr0008432	Ribitol	D-Ribulose	Not Available		VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Alzheimer's disease	Slight Increase	Association	Human Blood	HMDB	8595727
Alzheimer's disease	Slight Increase	Association	Human Cerebrospinal Fluid (CSF)	HMDB	8595727
Ribose-5-phosphate isomerase deficiency		Association	Human Urine	HMDB	14988808
Ribose-5-phosphate isomerase deficiency		Association	Human Blood	HMDB	14988808

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Spirochaetes	1		Microbial culture
Bacteria	Deinococcus-thermus	2		Microbial culture
Bacteria	Proteobacteria	24	Human ; Human mucosa; Human stool; Human supragingival plaque; Human feces; Human saliva; Human subgingival plaque	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Bacteroidetes	3	Human ; Human feces	Microbial culture
Bacteria	Actinobacteria	1		Microbial culture
Eukaryota/Fungi	Ascomycota	3	Human feces	Microbial culture
Bacteria	Firmicutes	3	Human feces	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen

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 Feces	Detected but not Quantified									HMDB
Human Blood	Detected and Quantified	0.55	0.08			uM	Elderly (>65 years old)	Both	Alzheimer's disease	HMDB	8595727
Human Cerebrospinal fluid (csf)	Detected and Quantified	3.8	0.68			uM	Elderly (>65 years old)	Both	Alzheimer's disease	HMDB	8595727
Human Urine	Detected and Quantified	154.5		123.0	186.0	umol/mmol creatinine	Newborn (0-30 days old)	Not Specified	Ribose-5-phosphate isomerase deficiency	HMDB	14988808
Human Blood	Detected and Quantified	20.0	6.0‚Äì35.0			uM	Adult (>18 years old)	Both	Ribose-5-phosphate isomerase deficiency	HMDB	14988808
Human Blood	Detected and Quantified	0.460		0.375	0.546	uM	Adult (>18 years old)	Both	Normal	HMDB	7710082
Human Blood	Detected and Quantified	0.54	0.078			uM	Elderly (>65 years old)	Both	Normal	HMDB	8595727
Human Cerebrospinal fluid (csf)	Detected and Quantified	17.8		0.0	35.6	uM	Adult (>18 years old)	Both	Normal	HMDB	18502700
Human Blood	Detected and Quantified	2.5		0.0	5.0	uM	Children (1-13 years old)	Both	Normal	HMDB	14988808
Human Cerebrospinal fluid (csf)	Detected and Quantified	3.64	0.67			uM	Elderly (>65 years old)	Both	Normal	HMDB	8595727
Human Cerebrospinal fluid (csf)	Detected and Quantified	3.73		3.01	4.45	uM	Adult (>18 years old)	Both	Normal	HMDB	7710082
Human Cerebrospinal fluid (csf)	Detected and Quantified	5.0		0.0	10.0	uM	Adult (>18 years old)	Not Specified	Normal	HMDB	11357181
Human Urine	Detected and Quantified	8.0		5.0	11.0	umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	HMDB	14988808
Human Urine	Detected and Quantified	3.5	2.24			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Urine	Detected and Quantified	3.533	2.267			umol/mmol creatinine	Not Specified	Not Specified	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Prostate	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	24029555
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	Normal	HMDB	29808030
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	28157703

External Links

HMDB ID

HMDB0000508

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

15963

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Georgescu C, Boboc F, Dumitrescu MR, Potcoava R, Florescu PD, Racovita D: [Identification of some atypical (morpho-cultural and enzymatic) characteristics of E. coli strains isolated in different clinical and epidemiological conditions]. Rev Ig Bacteriol Virusol Parazitol Epidemiol Pneumoftiziol Bacteriol Virusol Parazitol Epidemiol. 1980 Jan-Mar;25(1):17-26. [PubMed:6990452 ]
Malnick H: Anaerobiospirillum thomasii sp. nov., an anaerobic spiral bacterium isolated from the feces of cats and dogs and from diarrheal feces of humans, and emendation of the genus Anaerobiospirillum. Int J Syst Bacteriol. 1997 Apr;47(2):381-4. doi: 10.1099/00207713-47-2-381. [PubMed:9103625 ]
De Baere T, Wauters G, Kampfer P, Labit C, Claeys G, Verschraegen G, Vaneechoutte M: Isolation of Buttiauxella gaviniae from a spinal cord patient with urinary bladder pathology. J Clin Microbiol. 2002 Oct;40(10):3867-70. doi: 10.1128/JCM.40.10.3867-3870.2002. [PubMed:12354904 ]
Brenner DJ, Davis BR, Steigerwalt AG, Riddle CF, McWhorter AC, Allen SD, Farmer JJ 3rd, Saitoh Y, Fanning GR: Atypical biogroups of Escherichia coli found in clinical specimens and description of Escherichia hermannii sp. nov. J Clin Microbiol. 1982 Apr;15(4):703-13. doi: 10.1128/jcm.15.4.703-713.1982. [PubMed:7040466 ]
Herzog C, Wood HC, Noel I, Booth JC: Comparison of a new enzyme-linked immunosorbent assay method with counterimmunoelectrophoresis for detection of teichoic acid antibodies in sera from patients with Staphylococcus aureus infections. J Clin Microbiol. 1984 Apr;19(4):511-5. doi: 10.1128/jcm.19.4.511-515.1984. [PubMed:6715518 ]
Hickman-Brenner FW, Vohra MP, Huntley-Carter GP, Fanning GR, Lowery VA 3rd, Brenner DJ, Farmer JJ 3rd: Leminorella, a new genus of Enterobacteriaceae: identification of Leminorella grimontii sp. nov. and Leminorella richardii sp. nov. found in clinical specimens. J Clin Microbiol. 1985 Feb;21(2):234-9. doi: 10.1128/jcm.21.2.234-239.1985. [PubMed:3972991 ]
Hickman-Brenner FW, Fanning GR, Arduino MJ, Brenner DJ, Farmer JJ 3rd: Aeromonas schubertii, a new mannitol-negative species found in human clinical specimens. J Clin Microbiol. 1988 Aug;26(8):1561-4. doi: 10.1128/jcm.26.8.1561-1564.1988. [PubMed:3139706 ]
Konishi K, Yamagishi T, Sakamoto K: A Halophilic vibrio isolated from a case of chronic cholecystitis. Microbiol Immunol. 1981;25(12):1221-8. doi: 10.1111/j.1348-0421.1981.tb00132.x. [PubMed:7334940 ]
Brenner DJ, McWhorter AC, Kai A, Steigerwalt AG, Farmer JJ 3rd: Enterobacter asburiae sp. nov., a new species found in clinical specimens, and reassignment of Erwinia dissolvens and Erwinia nimipressuralis to the genus Enterobacter as Enterobacter dissolvens comb. nov. and Enterobacter nimipressuralis comb. nov. J Clin Microbiol. 1986 Jun;23(6):1114-20. doi: 10.1128/jcm.23.6.1114-1120.1986. [PubMed:3711302 ]
Funke G, Lucchini GM, Pfyffer GE, Marchiani M, von Graevenitz A: Characteristics of CDC group 1 and group 1-like coryneform bacteria isolated from clinical specimens. J Clin Microbiol. 1993 Nov;31(11):2907-12. doi: 10.1128/jcm.31.11.2907-2912.1993. [PubMed:8263175 ]
Aldova E, Hausner O, Kocmoud Z, Schindler J, Petras P: A new member of the family Enterobacteriaceae--Pragia fontium. J Hyg Epidemiol Microbiol Immunol. 1988;32(4):433-6. [PubMed:3221093 ]
McWhorter AC, Haddock RL, Nocon FA, Steigerwalt AG, Brenner DJ, Aleksic S, Bockemuhl J, Farmer JJ 3rd: Trabulsiella guamensis, a new genus and species of the family Enterobacteriaceae that resembles Salmonella subgroups 4 and 5. J Clin Microbiol. 1991 Jul;29(7):1480-5. doi: 10.1128/jcm.29.7.1480-1485.1991. [PubMed:1885744 ]
Podschun R: Phenotypic properties of Klebsiella pneumoniae and K. oxytoca isolated from different sources. Zentralbl Hyg Umweltmed. 1990 May;189(6):527-35. [PubMed:2200423 ]
Yoshioka S, Kameyama K, Sanaka M, Sekine I, Kagimoto S, Fujitsuka S, Saitoh S: Effect of diabetes on the free polyol pattern in cataractous lenses. Clin Chem. 1991 May;37(5):686-9. [PubMed:2032321 ]
Hudson MJ, Hollis DG, Weaver RE, Galvis CG: Relationship of CDC group EO-2 and psychrobacter immobilis. J Clin Microbiol. 1987 Oct;25(10):1907-10. doi: 10.1128/jcm.25.10.1907-1910.1987. [PubMed:3667912 ]
Brisse S, van Himbergen T, Kusters K, Verhoef J: Development of a rapid identification method for Klebsiella pneumoniae phylogenetic groups and analysis of 420 clinical isolates. Clin Microbiol Infect. 2004 Oct;10(10):942-5. doi: 10.1111/j.1469-0691.2004.00973.x. [PubMed:15373895 ]
Roboz J, Kappatos DC, Holland JF: Role of individual serum pentitol concentrations in the diagnosis of disseminated visceral candidiasis. Eur J Clin Microbiol. 1987 Dec;6(6):708-14. doi: 10.1007/BF02013083. [PubMed:3440465 ]
Roboz J, Kappatos DC, Greaves J, Holland JF: Determination of polyols in serum by selected ion monitoring. Clin Chem. 1984 Oct;30(10):1611-5. [PubMed:6434200 ]
Shetty HU, Holloway HW, Rapoport SI: Capillary gas chromatography combined with ion trap detection for quantitative profiling of polyols in cerebrospinal fluid and plasma. Anal Biochem. 1995 Jan 1;224(1):279-85. doi: 10.1006/abio.1995.1041. [PubMed:7710082 ]
Thaller MC, Berlutti F, Dainelli B, Pezzi R: New plate medium for screening and presumptive identification of gram-negative urinary tract pathogens. J Clin Microbiol. 1988 Apr;26(4):791-3. doi: 10.1128/jcm.26.4.791-793.1988. [PubMed:3366875 ]
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Huck JH, Roos B, Jakobs C, van der Knaap MS, Verhoeven NM: Evaluation of pentitol metabolism in mammalian tissues provides new insight into disorders of human sugar metabolism. Mol Genet Metab. 2004 Jul;82(3):231-7. doi: 10.1016/j.ymgme.2004.05.003. [PubMed:15234337 ]
Wamelink MM, Smith DE, Jakobs C, Verhoeven NM: Analysis of polyols in urine by liquid chromatography-tandem mass spectrometry: a useful tool for recognition of inborn errors affecting polyol metabolism. J Inherit Metab Dis. 2005;28(6):951-63. doi: 10.1007/s10545-005-0233-4. [PubMed:16435188 ]
Cavalli C, Teng C, Battaglia FC, Bevilacqua G: Free sugar and sugar alcohol concentrations in human breast milk. J Pediatr Gastroenterol Nutr. 2006 Feb;42(2):215-21. doi: 10.1097/01.mpg.0000189341.38634.77. [PubMed:16456418 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
Haga H, Nakajima T: Determination of polyol profiles in human urine by capillary gas chromatography. Biomed Chromatogr. 1989 Mar;3(2):68-71. doi: 10.1002/bmc.1130030206. [PubMed:2736321 ]
Verhoeven NM, Huck JH, Roos B, Struys EA, Salomons GS, Douwes AC, van der Knaap MS, Jakobs C: Transaldolase deficiency: liver cirrhosis associated with a new inborn error in the pentose phosphate pathway. Am J Hum Genet. 2001 May;68(5):1086-92. doi: 10.1086/320108. Epub 2001 Mar 27. [PubMed:11283793 ]
Huck JH, Verhoeven NM, Struys EA, Salomons GS, Jakobs C, van der Knaap MS: Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy. Am J Hum Genet. 2004 Apr;74(4):745-51. doi: 10.1086/383204. Epub 2004 Feb 25. [PubMed:14988808 ]

Showing metabocard for Ribitol (MMDBc0000110)

MOL for #<Metabolite:0x00007f46e14b4608>

3D MOL for #<Metabolite:0x00007f46e14b4608>

3D SDF for #<Metabolite:0x00007f46e14b4608>

3D-SDF for #<Metabolite:0x00007f46e14b4608>

PDB for #<Metabolite:0x00007f46e14b4608>

3D PDB for #<Metabolite:0x00007f46e14b4608>

SMILES for #<Metabolite:0x00007f46e14b4608>

INCHI for #<Metabolite:0x00007f46e14b4608>

Structure for #<Metabolite:0x00007f46e14b4608>

3D Structure for #<Metabolite:0x00007f46e14b4608>