MiMeDB: Showing metabocard for D-Arabinose (MMDBc0031892)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:53:46 UTC

Update Date

2024-10-17 18:49:11 UTC

Metabolite ID

MMDBc0031892

Metabolite Identification

Common Name

D-Arabinose

Description

Arabinose is an aldopentose ‚Äì a monosaccharide containing five carbon atoms, and including an aldehyde (CHO) functional group. (Wikipedia ) D-Arabinose is degraded by Escherichia coli B via some of the L-fucose pathway enzymes and a D-ribulokinase which is distinct from the L-fuculokinase of the L-fucose pathway. (PMID 3056899 )

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2S,3R,4R)-2,3,4,5-Tetrahydroxypentanal	ChEBI
(+/-)-arabinose	HMDB
Aloe sugar	HMDB
Aloinose	HMDB
DL-Arabinose	HMDB
Pectinose	HMDB
D-Arabinose	ChEBI

Molecular Formula

C₅H₁₀O₅

Average Mass

150.1299

Monoisotopic Mass

150.05282343

IUPAC Name

(2S,3R,4R)-2,3,4,5-tetrahydroxypentanal

Traditional Name

arabinose

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4-,5+/m1/s1

InChI Key

PYMYPHUHKUWMLA-WDCZJNDASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Beta-hydroxy aldehyde
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Short-chain aldehyde
Primary alcohol
Carbonyl group
Aldehyde
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

D-arabinose (CHEBI:46983 )
aldehydo-arabinose (CHEBI:46983 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	380 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2.9	ChemAxon
logS	0.4	ALOGPS
pKa (Strongest Acidic)	12.33	ChemAxon
pKa (Strongest Basic)	-3	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	31.38 m³·mol⁻¹	ChemAxon
Polarizability	13.42 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	splash10-052f-9100000000-3d844ea1b588172feaf0	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-05i0-6249400000-6324b88618b9174f1ee5	2017-10-06	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-08mi-9100000000-fdc6cb3672d0fd9782e4	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 10V, negative	splash10-0a4i-9000000000-8b4cbdfdbd1d64750afc	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 1V, negative	splash10-0002-1900000000-a6fad2b086e4d72e6455	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 4V, negative	splash10-000j-9500000000-7f3c671f5a2325c13521	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 8V, negative	splash10-052r-9000000000-4607894e05698b4efd4b	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 10V, negative	splash10-0a4r-9000000000-7713ba3bfd41873ed05b	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 14V, negative	splash10-0a4i-9000000000-19cc19a6070f8904f223	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 17V, negative	splash10-0a4i-9000000000-cbfe90fac8fd1f09d178	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 20V, negative	splash10-0a4i-9000000000-194cea61e7f4bb116108	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 10V, negative	splash10-001i-2900000000-0431fbb715edbb5c2854	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 0V, negative	splash10-001i-0900000000-9b7382416823533b7db1	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 0V, negative	splash10-001i-0900000000-b354fa776d3c927b52a8	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 0V, negative	splash10-001i-1900000000-4f54308f655454dcf238	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-001i-2900000000-ffb4e5e554a72f34fd7b	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-001i-4900000000-df24839373685cc97976	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-001r-7900000000-08514302c6b21ad9497c	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-008i-9700000000-9b73d2467b158cb7fe64	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, negative	splash10-00dr-9300000000-80b57725a8299b2e9afa	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-00dr-9100000000-f5eb0b039697ddead9f8	2020-07-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-2900000000-f8b9c6d77ac7485b2a13	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9300000000-c381cba09705c9d22367	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08fv-9000000000-157eda9875c5cd43b332	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000j-9400000000-8bb17d4c0bc5362b2610	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06ri-9200000000-f20b8cc45d0196859991	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-83841c4e2cbd5aa6df09	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0008365	D-Arabinose	D-Ribulose	Not Available	VMH	30371894
MMDBr0008376	D-Ribulose	D-Arabinose	Not Available	VMH	30371894
MMDBr0010899	D-Arabinose	D-Arabinose 5-phosphate	Not Available	VMH	30371894

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	46	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human sputum; Human subgingival plaque	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	92	Human feces; Human sputum; Human pleural fluid plaque; Human dental plaque; Human ; Human mucosa; Human nasopharyngeal swab; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Bacteria	Bacteroidetes	9	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Firmicutes	6	Human ; Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	2	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference
Food			FooDB	31437929
Food			FooDB	31437929
Food			FooDB	31437929
Food			FooDB	31437929
Plant	Plant	Solanum tuberosum	FooDB	31437929
Plant	Plant	Borago officinalis	FooDB	31437929
Plant	Plant	Malus pumila	FooDB	31437929
Plant	Fruit	Hippophae rhamnoides	FooDB	31437929
Plant	Seed	Sinapis alba	FooDB	31437929
Plant	Seed	Glycine max	FooDB	31437929
Plant	Bulb	Allium sativum l. var. sativum	FooDB	31437929
Plant	Plant	Taraxacum officinale	FooDB	31437929
Plant	Seed	Trigonella foenum-graecum	FooDB	31437929
Plant	Plant	Apium graveolens	FooDB	31437929
Plant	Rhizome	Curcuma longa	FooDB	31437929
Plant	Plant	Portulaca oleracea	FooDB	31437929
Plant	Fruit	Olea europaea	FooDB	31437929
Plant	Root	Daucus carota ssp. sativus	FooDB	31437929
Plant	Essential oil	Syzygium aromaticum	FooDB	31437929
Plant	Seed	Carum carvi	FooDB	31437929
Plant	Resin, exudate, sap	Anacardium occidentale	FooDB	31437929
Plant	Plant	Capparis spinosa	FooDB	31437929
Plant	Bulb	Allium cepa	FooDB	31437929
Plant	Fruit	Tamarindus indica	FooDB	31437929
Plant	Fruit	Psidium guajava	FooDB	31437929
Plant	Seed	Theobroma cacao	FooDB	31437929
Plant	Root	Colocasia esculenta	FooDB	31437929
Plant	Fruit	Ficus carica	FooDB	31437929
Plant	Wood	Ginkgo biloba	FooDB	31437929
Plant	Root	Daucus carota	FooDB	31437929
Plant	Fruit	Abelmoschus esculentus	FooDB	31437929
Plant	Fruit	Musa x paradisiaca	FooDB	31437929
Plant	Fruit	Phoenix dactylifera	FooDB	31437929
Plant	Seed	Coffea arabica	FooDB	31437929
Plant	Seed	Helianthus annuus	FooDB	31437929

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected and Quantified	1041.0984	657.431	nmol/g wet feces	Not Specified	Not Specified	Normal	HMDB	20669995
Human Feces	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	20669995
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	Colorectal Cancer	HMDB	27275383
Human Feces	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	20669995
Human Feces	Detected but not Quantified				Infant (0-1 year old)	Both	Normal	HMDB	22411374

External Links

HMDB ID

HMDB0029942

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001219

KNApSAcK ID

Not Available

Chemspider ID

59687

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Arabinose

METLIN ID

Not Available

PubChem Compound

66308

PDB ID

Not Available

ChEBI ID

46983

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 D-Arabinose (MMDBc0031892)

MOL for #<Metabolite:0x00007fab18c377e0>

3D MOL for #<Metabolite:0x00007fab18c377e0>

3D SDF for #<Metabolite:0x00007fab18c377e0>

3D-SDF for #<Metabolite:0x00007fab18c377e0>

PDB for #<Metabolite:0x00007fab18c377e0>

3D PDB for #<Metabolite:0x00007fab18c377e0>

SMILES for #<Metabolite:0x00007fab18c377e0>

INCHI for #<Metabolite:0x00007fab18c377e0>

Structure for #<Metabolite:0x00007fab18c377e0>

3D Structure for #<Metabolite:0x00007fab18c377e0>