MiMeDB: Showing metabocard for D-Ribulose (MMDBc0000530)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:39:51 UTC

Update Date

2024-04-30 19:32:49 UTC

Metabolite ID

MMDBc0000530

Metabolite Identification

Common Name

D-Ribulose

Description

D-Ribulose (CAS: 488-84-6) is a ketopentose - a monosaccharide containing five carbon atoms, including a ketone functional group. D-Ribulose is an intermediate in the fungal pathway for D-arabitol production. As the 1,5-bisphosphate, it combines with CO2 at the start of the photosynthetic process in green plants (carbon dioxide trap). D-Ribulose is the epimer of D-xylulose (Wikipedia ). Ribulose is also a microbial metabolite found in Acetobacter and Gluconobacter (PMID: 16232643 , 11272814 ).

Structure

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

Synonyms

Value	Source
D(-)-Ribulose	HMDB
D-Adonose	HMDB
D-Arabinulose	HMDB
D-Araboketose	HMDB
D-Erythropentulose	HMDB
D-Ribosone	HMDB
D-Erythro-2-ketopentose	HMDB
D-Erythro-pentulose	HMDB
beta-D-Ribulofuranose	HMDB
beta-D-Ribulose	HMDB
beta-D-Erythro-2-pentulofuranose	HMDB
Β-D-ribulofuranose	HMDB
Β-D-ribulose	HMDB
Β-D-erythro-2-pentulofuranose	HMDB
D-Ribulose	HMDB

Molecular Formula

C₅H₁₀O₅

Average Mass

150.13

Monoisotopic Mass

150.052823422

IUPAC Name

(2R,3R,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol

Traditional Name

(2R,3R,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4-,5-/m1/s1

InChI Key

LQXVFWRQNMEDEE-UOWFLXDJSA-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
Oxolane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1310 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.1	ChemAxon
logS	0.94	ALOGPS
pKa (Strongest Acidic)	10.29	ChemAxon
pKa (Strongest Basic)	-3.5	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	1	ChemAxon
Refractivity	30.4 m³·mol⁻¹	ChemAxon
Polarizability	13.38 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
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	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-052b-8900000000-6174ea340f73118a4e71	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9000000000-3155b6a3b975db3bc626	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9000000000-cc7ea805a3871cd388b5	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-2900000000-d014866a9eaa4bcc1c15	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-05fv-9000000000-fac868271cf0145b751c	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052e-9000000000-3310acb8673d3f763bfa	2021-09-25	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

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces
Fibroblasts
Placenta

Tissue Locations

Fibroblasts
Placenta

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
MMDBr0002060	D-Ribulose	D-Ribulose 5-phosphate	Not Available	VMH	15234337
MMDBr0007138	D-Ribulose	D-Ribulose 5-phosphate	Not Available	VMH; KEGG	30371894
MMDBr0008365	D-Arabinose	D-Ribulose	Not Available	VMH	30371894
MMDBr0008376	D-Ribulose	D-Arabinose	Not Available	VMH	30371894
MMDBr0008432	Ribitol	D-Ribulose	Not Available	VMH	30371894
MMDBr0010902	D-Ribose	D-Ribulose	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	Actinobacteria	102	Human ; Human feces; Human saliva; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human supragingival plaque; Human subgingival plaque; Human mucosa	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	199	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Firmicutes	272	Human stool; Human ; Human feces; Human pleural fluid plaque; Pig ; Human subgingival plaque; Human saliva; Cattle	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Bacteroidetes	95	Human feces; Human appendix biopsy; Human stool; Human saliva; Human ; Human gastric fluid; Human urine; Human subgingival plaque	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	3	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	3		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Basidiomycota	1
Eukaryota/Fungi	Ascomycota	5	Human feces
Bacteria	Cyanobacteria	1
Bacteria	Thermotogae	1

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	HMDB	27275383
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Fibroblasts	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0000621

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Ribulose

METLIN ID

Not Available

PubChem Compound

12358756

PDB ID

Not Available

ChEBI ID

17173

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Ito M, Amano H, Yanagisawa I: Ribulose-peptide in human semen: II. Synthesis. Arch Androl. 1978;1(1):77-82. doi: 10.3109/01485017808988321. [PubMed:570380 ]
Adachi O, Fujii Y, Ano Y, Moonmangmee D, Toyama H, Shinagawa E, Theeragool G, Lotong N, Matsushita K: Membrane-bound sugar alcohol dehydrogenase in acetic acid bacteria catalyzes L-ribulose formation and NAD-dependent ribitol dehydrogenase is independent of the oxidative fermentation. Biosci Biotechnol Biochem. 2001 Jan;65(1):115-25. doi: 10.1271/bbb.65.115. [PubMed:11272814 ]
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 ]
Ahmed Z, Shimonishi T, Bhuiyan SH, Utamura M, Takada G, Izumori K: Biochemical preparation of L-ribose and L-arabinose from ribitol: a new approach. J Biosci Bioeng. 1999;88(4):444-8. doi: 10.1016/s1389-1723(99)80225-4. [PubMed:16232643 ]
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 ]

Showing metabocard for D-Ribulose (MMDBc0000530)

MOL for #<Metabolite:0x00007fdb3a9e2b50>

3D MOL for #<Metabolite:0x00007fdb3a9e2b50>

3D SDF for #<Metabolite:0x00007fdb3a9e2b50>

3D-SDF for #<Metabolite:0x00007fdb3a9e2b50>

PDB for #<Metabolite:0x00007fdb3a9e2b50>

3D PDB for #<Metabolite:0x00007fdb3a9e2b50>

SMILES for #<Metabolite:0x00007fdb3a9e2b50>

INCHI for #<Metabolite:0x00007fdb3a9e2b50>

Structure for #<Metabolite:0x00007fdb3a9e2b50>

3D Structure for #<Metabolite:0x00007fdb3a9e2b50>