MiMeDB: Showing metabocard for 5-deoxy-D-glucuronic acid (MMDBc0055557)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:58:49 UTC

Update Date

2025-10-07 16:09:11 UTC

Metabolite ID

MMDBc0055557

Metabolite Identification

Common Name

5-deoxy-D-glucuronic acid

Description

5-deoxy-D-glucuronic acid is a carbohydrate metabolite belonging to the class of uronic acids. Its chemical structure features a six-carbon backbone similar to D-glucuronic acid, but with a hydroxyl group replaced by a hydrogen atom at the 5-position, resulting in a unique configuration. This compound is involved in various biochemical pathways, particularly in the metabolism of carbohydrates. For instance, it is produced during the hydrolysis of 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione, a reaction catalyzed by the enzyme IolD (PMID:18310071 ). Additionally, 5-deoxy-D-glucuronic acid undergoes isomerization by the enzyme IolB, leading to the formation of 2-deoxy-5-keto-D-gluconic acid (PMID:18310071 ). These enzymatic reactions highlight its role in the degradation and transformation of complex carbohydrates, contributing to the broader understanding of metabolic pathways in organisms.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221582D          

 15 14  0  0  1  0            999 V2000
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6039   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.5395    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  2  2  0  0  0  0
  3  8  1  6  0  0  0
  4  9  1  6  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
  6 12  1  6  0  0  0
  3 13  1  6  0  0  0
  4 14  1  6  0  0  0
  6 15  1  6  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0055557

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CC([O-])=O)[C@]([H])(O)[C@@]([H])(O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h2-4,6,8-9,12H,1H2,(H,10,11)/p-1/t3-,4+,6+/m1/s1

> <INCHI_KEY>
HPITTXOWHLWIEK-IWGUZYHVSA-M

> <FORMULA>
C6H9O6

> <MOLECULAR_WEIGHT>
177.133

> <EXACT_MASS>
177.04046159

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.846904462252589

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-3,4,5-trihydroxy-6-oxohexanoate

> <JCHEM_LOGP>
-2.5329275643333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.397048884621881

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8220991782056357

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3039209223332655

> <JCHEM_POLAR_SURFACE_AREA>
117.89000000000001

> <JCHEM_REFRACTIVITY>
46.7119

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
5-deoxy-D-glucuronate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         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-1
HETATM   12  O   UNK     0       2.874   2.310   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       4.207   1.540   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       1.540   1.540   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       2.874  -0.770   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4    7                                                       
CONECT    3    1    6    8   13                                             
CONECT    4    2    6    9   14                                             
CONECT    5    1   10   11                                                  
CONECT    6    3    4   12   15                                             
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    3                                                            
CONECT   14    4                                                            
CONECT   15    6                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
(3R,4S,5R)-3,4,5-Trihydroxy-6-oxohexanoate	ChEBI
(3R,4S,5R)-3,4,5-Trihydroxy-6-oxohexanoic acid	Generator
5-Deoxy-D-glucuronic acid	Generator

Molecular Formula

C₆H₉O₆

Average Mass

177.133

Monoisotopic Mass

177.04046159

IUPAC Name

(3R,4S,5R)-3,4,5-trihydroxy-6-oxohexanoate

Traditional Name

5-deoxy-D-glucuronate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CC([O-])=O)[C@]([H])(O)[C@@]([H])(O)C=O

InChI Identifier

InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h2-4,6,8-9,12H,1H2,(H,10,11)/p-1/t3-,4+,6+/m1/s1

InChI Key

HPITTXOWHLWIEK-IWGUZYHVSA-M

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 hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Sugar acid
Hydroxy fatty acid
Beta-hydroxy aldehyde
Fatty acyl
Fatty acid
Hydroxy acid
Monosaccharide
Alpha-hydroxyaldehyde
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Polyol
Monocarboxylic acid or derivatives
Alcohol
Carbonyl group
Hydrocarbon derivative
Aldehyde
Organic oxide
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

carbohydrate acid anion (CHEBI:58852 )
monocarboxylic acid anion (CHEBI:58852 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.5	ChemAxon
pKa (Strongest Acidic)	3.82	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	117.89 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	46.71 m³·mol⁻¹	ChemAxon
Polarizability	14.85 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

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	260.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	203.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	55.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	295.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	268.2
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	333.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	828.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	229.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	933.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	172.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	266.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	184.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	47.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	402.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	679.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	69.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	235.2
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	934.5
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	626.5

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_1	C[Si](C)(C)O[C@H](CC(=O)[O-])[C@H](O)[C@@H](O)C=O	standard non polar	2025-10-24	1654.69
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_2	C[Si](C)(C)O[C@H]([C@@H](O)C=O)[C@H](O)CC(=O)[O-]	standard non polar	2025-10-24	2125.59
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_3	C[Si](C)(C)O[C@@H](C=O)[C@@H](O)[C@H](O)CC(=O)[O-]	standard non polar	2025-10-24	1880.92
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_4	C[Si](C)(C)OC=C(O)[C@@H](O)[C@H](O)CC(=O)[O-]	standard non polar	2025-10-24	1892.3
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_5	C[Si](C)(C)O[C@H](CC(=O)[O-])[C@H](O[Si](C)(C)C)[C@@H](O)C=O	standard non polar	2025-10-24	1954.05
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_6	C[Si](C)(C)O[C@@H](C=O)[C@@H](O)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2594.42
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_7	C[Si](C)(C)OC=C(O)[C@@H](O)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2321.17
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_8	C[Si](C)(C)O[C@@H]([C@H](O)CC(=O)[O-])[C@H](C=O)O[Si](C)(C)C	standard non polar	2025-10-24	1735.43
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_9	C[Si](C)(C)OC=C(O)[C@@H](O[Si](C)(C)C)[C@H](O)CC(=O)[O-]	standard non polar	2025-10-24	1873.57
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_10	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O)[C@H](O)CC(=O)[O-]	standard non polar	2025-10-24	1818.24
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_11	C[Si](C)(C)O[C@H]([C@H](C=O)O[Si](C)(C)C)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2100.86
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_12	C[Si](C)(C)OC=C(O)[C@@H](O[Si](C)(C)C)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2100.56
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_13	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2220.23
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_14	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O)CC(=O)[O-]	standard non polar	2025-10-24	2175.11
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_15	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2009.81
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_1	C[Si](C)(C)O[C@H](CC(=O)[O-])[C@H](O)[C@@H](O)C=O	standard polar	2025-10-24	1883.39
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_2	C[Si](C)(C)O[C@H]([C@@H](O)C=O)[C@H](O)CC(=O)[O-]	standard polar	2025-10-24	1857.56
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_3	C[Si](C)(C)O[C@@H](C=O)[C@@H](O)[C@H](O)CC(=O)[O-]	standard polar	2025-10-24	2430.76
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_4	C[Si](C)(C)OC=C(O)[C@@H](O)[C@H](O)CC(=O)[O-]	standard polar	2025-10-24	2280.16
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_5	C[Si](C)(C)O[C@H](CC(=O)[O-])[C@H](O[Si](C)(C)C)[C@@H](O)C=O	standard polar	2025-10-24	1668.89
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_6	C[Si](C)(C)O[C@@H](C=O)[C@@H](O)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard polar	2025-10-24	1790.29
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_7	C[Si](C)(C)OC=C(O)[C@@H](O)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard polar	2025-10-24	2475.89
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_8	C[Si](C)(C)O[C@@H]([C@H](O)CC(=O)[O-])[C@H](C=O)O[Si](C)(C)C	standard polar	2025-10-24	2096.63
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_9	C[Si](C)(C)OC=C(O)[C@@H](O[Si](C)(C)C)[C@H](O)CC(=O)[O-]	standard polar	2025-10-24	2037.53
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_10	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O)[C@H](O)CC(=O)[O-]	standard polar	2025-10-24	2327.64
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_11	C[Si](C)(C)O[C@H]([C@H](C=O)O[Si](C)(C)C)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard polar	2025-10-24	2552.49
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_12	C[Si](C)(C)OC=C(O)[C@@H](O[Si](C)(C)C)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard polar	2025-10-24	2214.67
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_13	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard polar	2025-10-24	1859.42
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_14	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O)CC(=O)[O-]	standard polar	2025-10-24	2012.26
Gas Chromatography	5-deoxy-D-glucuronic acid_TMS_15	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H](CC(=O)[O-])O[Si](C)(C)C	standard polar	2025-10-24	2055.85

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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/Eubacteria	Firmicutes	27	Human feces; Human ; Human supragingival plaque; Catfish

Exposure Sources

Other Exposures

Source Type	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

26331400

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46878459

PDB ID

Not Available

ChEBI ID

58852

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

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 5-deoxy-D-glucuronic acid (MMDBc0055557)

MOL for #<Metabolite:0x00007f2dffef5590>

3D MOL for #<Metabolite:0x00007f2dffef5590>

3D SDF for #<Metabolite:0x00007f2dffef5590>

3D-SDF for #<Metabolite:0x00007f2dffef5590>

PDB for #<Metabolite:0x00007f2dffef5590>

3D PDB for #<Metabolite:0x00007f2dffef5590>

SMILES for #<Metabolite:0x00007f2dffef5590>

INCHI for #<Metabolite:0x00007f2dffef5590>

Structure for #<Metabolite:0x00007f2dffef5590>

3D Structure for #<Metabolite:0x00007f2dffef5590>