MiMeDB: Showing metabocard for 3-Dehydro-L-gulonate (MMDBc0029825)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:43:16 UTC

Update Date

2022-08-31 17:18:54 UTC

Metabolite ID

MMDBc0029825

Metabolite Identification

Common Name

3-Dehydro-L-gulonate

Description

3-Dehydro-L-gulonate is an intermediate in ascorbic acid degradation. It is a substrate for the enzyme 2,3-diketo-L-gulonate reductase. This enzyme catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH, to form 3-keto-L-gulonate. It participates in the reaction: 3-dehydro-L-gulonate + NAD(P)+ = (4R,5S)-4,5,6-trihydroxy-2,3-dioxohexanoate + NAD(P)H. Several pathways for the irreversible catabolism of ascorbate have been described. Facultatively aerobic bacteria such as Escherichia coli degrade L-ascorbate by different pathways under aerobic and anaerobic conditions. The anaerobic pathway begins with phosphorylation of ascorbate (mediated by a PTS-type transporter), while the aerobic pathway proceeds via 2,3-dioxo-L-gulonate. Both pathways produce D-xylulose 5-phosphate, a centeral metabolite that is fed into the pentose phosphate pathway.

Structure

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

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      32.061  -9.805   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.727  -5.955   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      28.059  -7.495   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      34.728  -9.805   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      33.394  -5.955   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      37.395  -8.265   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      36.062  -5.955   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      32.061  -8.265   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.727  -7.495   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      33.394  -7.495   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.393  -8.265   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      34.728  -8.265   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      36.062  -7.495   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3   11                                                            
CONECT    4   12                                                            
CONECT    5   10                                                            
CONECT    6   13                                                            
CONECT    7   13                                                            
CONECT    8    1    9   10                                                  
CONECT    9    2    8   11                                                  
CONECT   10    5    8   12                                                  
CONECT   11    3    9                                                       
CONECT   12    4   10   13                                                  
CONECT   13    6    7   12                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
3-Dehydro-L-gulonic acid	Generator
L-Xylo-hex-3-ulosonic acid	HMDB

Molecular Formula

C₆H₁₀O₇

Average Mass

194.1394

Monoisotopic Mass

194.042652674

IUPAC Name

(2S,4R,5S)-2,4,5,6-tetrahydroxy-3-oxohexanoic acid

Traditional Name

3-dehydro-L-gulonic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,5,7-9,11H,1H2,(H,12,13)/t2-,3+,5-/m0/s1

InChI Key

WTAHRPBPWHCMHW-LWKDLAHASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Hexose monosaccharide
Medium-chain keto acid
Beta-keto acid
Sugar acid
Acyloin
Alpha-hydroxy acid
Beta-hydroxy ketone
Hydroxy acid
Keto acid
1,3-dicarbonyl compound
Monosaccharide
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Polyol
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid (CHEBI:16142 )
hexonic acid (CHEBI:16142 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	105 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-2.6	ChemAxon
logS	-0.27	ALOGPS
pKa (Strongest Acidic)	3.16	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	135.29 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	37.58 m³·mol⁻¹	ChemAxon
Polarizability	16.3 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	splash10-0r29-9200000000-bfa5f284c8a99449827a	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positive	splash10-00ku-4401960000-e7040dc9b253756697ac	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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-2900000000-4ee99057131bac58d24b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0imi-9600000000-abad7f2422697e8886ed	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9100000000-7128eed92da683639fe8	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-05bu-9800000000-2f48ad5aa2d38b4abf96	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ap0-9500000000-96092591d92e04b163ef	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4r-9100000000-833ef232e8c397c98dd3	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00fr-9300000000-904e9656bc69e6510b01	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a6r-9100000000-dc8c8d7f3d7b9cbccc90	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-4026211091bf9f90ad00	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00dl-9700000000-a0000aecbfc4c59cdcd5	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0cml-9200000000-df3574dae2a7dfc61329	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08fr-9000000000-4d49c4220ff5afa3bdaf	2021-09-22	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

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
MMDBp0196553	Lambda-crystallin homolog	Unknown	Q9Y2S2	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0000664	3-Dehydro-L-gulonate	Carbon dioxide	Not Available	Dehydro-L-Gulonate Decarboxylase	VMH	6821187
MMDBr0001396	L-Gulonate	3-Dehydro-L-gulonate	Not Available	L-Gulonate 3-Dehydrogenase	VMH	30371894
MMDBr0007678	3-Dehydro-L-gulonate	2,3-Diketo-L-gulonate	Not Available	3-Dehydro-L-gulonate:NAD+ 2-oxidoreductase	VMH	30371894
MMDBr0007753	2,3-Diketo-L-gulonate	3-Dehydro-L-gulonate	Not Available	2,3 dioxo-L-gulonate reductase	VMH	30371894
MMDBr0014154	3-Dehydro-L-gulonate	2,3-Diketo-L-gulonate	2,3-diketo-L-gulonate reductase	Reduction	RHEA	34755880
MMDBr0014155	3-Dehydro-L-gulonate	2,3-Diketo-L-gulonate	2,3-diketo-L-gulonate reductase	Reduction	RHEA	34755880
MMDBr0014800	3-Dehydro-L-gulonate	3-Dehydro-L-gulonate 6-phosphate	L-xylulose/3-keto-L-gulonate kinase	Phosphorylation	RHEA	34755880
MMDBr0014801	3-Dehydro-L-gulonate	3-Dehydro-L-gulonate 6-phosphate	L-xylulose/3-keto-L-gulonate kinase	Phosphorylation	RHEA	34755880
MMDBr0018150	Adenosine triphosphate	Hydrogen Ion	L-xylulose/3-keto-L-gulonate kinase	Phosphorylation	PathBank	31602464
MMDBr0018151	Hydrogen Ion	NAD	2,3-diketo-L-gulonate reductase	Reduction	PathBank	31602464

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	67	Pig ; Human feces; Human ; Human stool; Human feces; pleural fluid plaque; bal; Human subgingival plaque; Chicken	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	14	Human feces	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction

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

External Links

HMDB ID

HMDB0006334

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023894

KNApSAcK ID

Not Available

Chemspider ID

388406

KEGG Compound ID

C00618

BioCyc ID

Not Available

BiGG ID

35509

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439273

PDB ID

Not Available

ChEBI ID

16142

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 ]

Showing metabocard for 3-Dehydro-L-gulonate (MMDBc0029825)

MOL for #<Metabolite:0x000055d249394c40>

3D MOL for #<Metabolite:0x000055d249394c40>

3D SDF for #<Metabolite:0x000055d249394c40>

3D-SDF for #<Metabolite:0x000055d249394c40>

PDB for #<Metabolite:0x000055d249394c40>

3D PDB for #<Metabolite:0x000055d249394c40>

SMILES for #<Metabolite:0x000055d249394c40>

INCHI for #<Metabolite:0x000055d249394c40>

Structure for #<Metabolite:0x000055d249394c40>

3D Structure for #<Metabolite:0x000055d249394c40>