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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2022-09-09 21:02:34 UTC

Update Date

2022-09-22 18:35:14 UTC

HMDB ID

HMDB0341414

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-Dehydro-2-deoxygluconic acid

Description

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       5.541   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.875   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.127   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.207  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.208   0.770   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.875  -1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.874   2.310   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    7                                                       
CONECT    3    1    6    8                                                  
CONECT    4    2    6    9                                                  
CONECT    5    1   10   11                                                  
CONECT    6    3    4   12                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Dehydro-2-deoxy-D-gluconic acid	Generator

Chemical Formula

C₆H₁₀O₆

Average Molecular Weight

178.14

Monoisotopic Molecular Weight

178.047738052

IUPAC Name

4,5,6-trihydroxy-3-oxohexanoic acid

Traditional Name

4,5,6-trihydroxy-3-oxohexanoic acid

CAS Registry Number

Not Available

SMILES

OCC(O)C(O)C(=O)CC(O)=O

InChI Identifier

InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h4,6-7,9,12H,1-2H2,(H,10,11)

InChI Key

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2	ALOGPS
logP	-1.9	ChemAxon
logS	0.07	ALOGPS
pKa (Strongest Acidic)	3.75	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	36.24 m³·mol⁻¹	ChemAxon
Polarizability	15.51 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

Predicted Chromatographic Properties

Predicted Retention Times

Not Available

Predicted Kovats Retention Indices

Not Available

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Dehydro-2-deoxygluconic acid GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2022-08-08	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Dehydro-2-deoxygluconic acid 10V, Positive-QTOF	splash10-03di-2900000000-642decf396af7b5cc277	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Dehydro-2-deoxygluconic acid 20V, Positive-QTOF	splash10-03di-9500000000-1d75fdeb0386f041e732	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Dehydro-2-deoxygluconic acid 40V, Positive-QTOF	splash10-06r6-9100000000-910031343a7cd5b307a3	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Dehydro-2-deoxygluconic acid 10V, Negative-QTOF	splash10-066r-6900000000-560ccb74a7e1bb8c5090	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Dehydro-2-deoxygluconic acid 20V, Negative-QTOF	splash10-0ab9-9300000000-15062933572e0ceb3f15	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Dehydro-2-deoxygluconic acid 40V, Negative-QTOF	splash10-0ab9-9000000000-4db43b76044f589b7e8f	2015-09-15	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

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

C03926

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

627

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Meister I, Zhang P, Sinha A, Skold CM, Wheelock AM, Izumi T, Chaleckis R, Wheelock CE: High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology. Anal Chem. 2021 Mar 30;93(12):5248-5258. doi: 10.1021/acs.analchem.1c00203. Epub 2021 Mar 19. [PubMed:33739820 ]

Showing metabocard for 3-Dehydro-2-deoxygluconic acid (HMDB0341414)

MOL for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

3D MOL for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

3D SDF for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

3D-SDF for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

PDB for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

3D PDB for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

SMILES for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

INCHI for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

Structure for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

3D Structure for HMDB0341414 (3-Dehydro-2-deoxygluconic acid)

Predicted Retention Times

Predicted Kovats Retention Indices

GC-MS Spectra

MS/MS Spectra

NMR Spectra