MiMeDB: Showing metabocard for L-Ribose (MMDBc0030133)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:55:11 UTC

Update Date

2022-08-31 17:39:58 UTC

Metabolite ID

MMDBc0030133

Metabolite Identification

Common Name

L-Ribose

Description

Ribose is an organic compound that occurs widely in nature. It is an aldopentose, a monosaccharide containing five carbon atoms that in its acyclic form has an aldehyde functional group at one end. Typically, ribose exists in the cyclic form. It comprises the backbone of RNA, a biopolymer that is the basis of genetic transcription. It is related to deoxyribose, as found in DNA, by the removal of one hydroxy group. Once phosphorylated, ribose can become a subunit of ATP, NADH, and several other compounds that are critical to metabolism. Ribose exists in two enantiomeric forms, primarily as D-ribose. L-ribose is the synthetic mirror image of D-ribose. (Wikipedia ) In E. coli, L-ribose can act as an competitive inhibitor of glucose dehydrogenase. (EcoCyc)

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    6                                                       
CONECT    2    4    7                                                       
CONECT    3    1    5    8   11                                             
CONECT    4    2    5    9   12                                             
CONECT    5    3    4   10   13                                             
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    5                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
(2S,3S,4S)-2,3,4,5-Tetrahydroxypentanal	ChEBI

Molecular Formula

C₅H₁₀O₅

Average Mass

150.1299

Monoisotopic Mass

150.05282343

IUPAC Name

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

Traditional Name

L-ribose

CAS Registry Number

24259-59-4

SMILES

[H][C@](O)(CO)[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-MROZADKFSA-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

aldehydo-ribose (CHEBI:47015 )
L-ribose (CHEBI:47015 )

Functional Ontology

Not Available

Physical Properties

State

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)	11.87	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	13.38 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 (TMS_3_9) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-2900000000-d4b4d16fe2bdea6dccd0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9300000000-be87d057e4e6e95de7e5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08fv-9000000000-9a3060e3aacc77a20cca	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000j-9400000000-dbd7597b23c261cf03b1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06ri-9200000000-bf3ea96e46d76c202a29	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-6b0fd940d309cdea3a46	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Not Available

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Ribose

METLIN ID

Not Available

PubChem Compound

90428

PDB ID

Not Available

ChEBI ID

47015

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]

Showing metabocard for L-Ribose (MMDBc0030133)

MOL for #<Metabolite:0x00007fed1590bf78>

3D MOL for #<Metabolite:0x00007fed1590bf78>

3D SDF for #<Metabolite:0x00007fed1590bf78>

3D-SDF for #<Metabolite:0x00007fed1590bf78>

PDB for #<Metabolite:0x00007fed1590bf78>

3D PDB for #<Metabolite:0x00007fed1590bf78>

SMILES for #<Metabolite:0x00007fed1590bf78>

INCHI for #<Metabolite:0x00007fed1590bf78>

Structure for #<Metabolite:0x00007fed1590bf78>

3D Structure for #<Metabolite:0x00007fed1590bf78>