MiMeDB: Showing metabocard for D-glucaro-1,5-lactone (MMDBc0055864)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:11 UTC

Update Date

2025-10-07 16:09:25 UTC

Metabolite ID

MMDBc0055864

Metabolite Identification

Common Name

D-glucaro-1,5-lactone

Description

D-glucaro-1,5-lactone is a lactone, specifically a cyclic ester derived from D-glucaric acid. Its chemical structure features a five-membered ring formed by the intramolecular esterification of the carboxylic acid and hydroxyl groups of D-glucaric acid. This compound has been implicated in various biochemical pathways, particularly in the context of glycosaminoglycan metabolism. Notably, D-glucaro-1,5-lactone has been shown to exhibit a high binding affinity to D-glucuronic acid and its substrate intermediates, including D-glucaro-1,4-lactone, as evidenced by studies on Q14F, S36L, and S75T mutants (PMID:31472210 ). Additionally, it has been identified as a potent inhibitor of beta-D-glucuronidase, suggesting its role in modulating glucuronidation processes, which are crucial for the detoxification of various substances in the body (PMID:3779687 ). The lactone's involvement in these pathways highlights its potential significance in metabolic regulation and enzymatic activity related to glucuronidation.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222092D          

 17 17  0  0  1  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  5  1  1  0  0  0
  6  3  1  0  0  0  0
  1  7  1  6  0  0  0
  2  8  1  1  0  0  0
  3  9  1  1  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  4  1  0  0  0  0
 13  6  1  0  0  0  0
  1 14  1  1  0  0  0
  2 15  1  6  0  0  0
  3 16  1  6  0  0  0
  4 17  1  1  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0055864

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)C(=O)O[C@]([H])(C([O-])=O)[C@@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,7-9H,(H,10,11)/p-1/t1-,2-,3+,4-/m0/s1

> <INCHI_KEY>
YLKFQNUGXOLRNI-QDQPNEQZSA-M

> <FORMULA>
C6H7O7

> <MOLECULAR_WEIGHT>
191.116

> <EXACT_MASS>
191.019726145

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
15.150724344954043

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxooxane-2-carboxylate

> <JCHEM_LOGP>
-2.4249986480000003

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.624958052393973

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.050629804599829

> <JCHEM_PKA_STRONGEST_BASIC>
-3.731615292386288

> <JCHEM_POLAR_SURFACE_AREA>
127.11999999999999

> <JCHEM_REFRACTIVITY>
45.4833

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxooxane-2-carboxylate

> <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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       2.667  -1.540   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
CONECT    1    2    3    7   14                                             
CONECT    2    1    4    8   15                                             
CONECT    3    1    6    9   16                                             
CONECT    4    2    5   13   17                                             
CONECT    5    4   10   11                                                  
CONECT    6    3   12   13                                                  
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    4    6                                                       
CONECT   14    1                                                            
CONECT   15    2                                                            
CONECT   16    3                                                            
CONECT   17    4                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

Synonyms

Value	Source
D-Glucaro-1,5-lactone	ChEBI

Molecular Formula

C₆H₇O₇

Average Mass

191.116

Monoisotopic Mass

191.019726145

IUPAC Name

(2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxooxane-2-carboxylate

Traditional Name

(2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxooxane-2-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)C(=O)O[C@]([H])(C([O-])=O)[C@@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C6H8O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,7-9H,(H,10,11)/p-1/t1-,2-,3+,4-/m0/s1

InChI Key

YLKFQNUGXOLRNI-QDQPNEQZSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gluconolactones. These are polyhydroxy acids containing a gluconolactone molecule, which is characterized by a tetrahydropyran substituted by three hydroxyl groups, one ketone group, and one hydroxymethyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Gluconolactones

Alternative Parents

Substituents

Gluconolactone
Beta-hydroxy acid
Delta valerolactone
Delta_valerolactone
Dicarboxylic acid or derivatives
Hydroxy acid
Pyran
Oxane
Carboxylic acid ester
Secondary alcohol
Lactone
Organoheterocyclic compound
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Polyol
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

carbohydrate acid anion (CHEBI:83384 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.4	ChemAxon
pKa (Strongest Acidic)	3.05	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	127.12 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	45.48 m³·mol⁻¹	ChemAxon
Polarizability	15.15 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	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-glucaro-1,5-lactone_TMS_1	C[Si](C)(C)O[C@H]1C(=O)O[C@H](C(=O)[O-])[C@@H](O)[C@@H]1O	standard non polar	2025-10-24	2376.98
Gas Chromatography	D-glucaro-1,5-lactone_TMS_2	C[Si](C)(C)O[C@@H]1[C@@H](C(=O)[O-])OC(=O)[C@H](O)[C@H]1O	standard non polar	2025-10-24	1985.18
Gas Chromatography	D-glucaro-1,5-lactone_TMS_3	C[Si](C)(C)O[C@@H]1[C@@H](O)C(=O)O[C@H](C(=O)[O-])[C@H]1O	standard non polar	2025-10-24	1979.11
Gas Chromatography	D-glucaro-1,5-lactone_TMS_4	C[Si](C)(C)O[C@@H]1[C@@H](C(=O)[O-])OC(=O)[C@H](O[Si](C)(C)C)[C@H]1O	standard non polar	2025-10-24	1687.32
Gas Chromatography	D-glucaro-1,5-lactone_TMS_5	C[Si](C)(C)O[C@@H]1[C@@H](O[Si](C)(C)C)C(=O)O[C@H](C(=O)[O-])[C@H]1O	standard non polar	2025-10-24	1696.5
Gas Chromatography	D-glucaro-1,5-lactone_TMS_6	C[Si](C)(C)O[C@@H]1[C@@H](C(=O)[O-])OC(=O)[C@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1810.66
Gas Chromatography	D-glucaro-1,5-lactone_TMS_7	C[Si](C)(C)O[C@@H]1[C@@H](O[Si](C)(C)C)C(=O)O[C@H](C(=O)[O-])[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1671.34
Gas Chromatography	D-glucaro-1,5-lactone_TMS_1	C[Si](C)(C)O[C@H]1C(=O)O[C@H](C(=O)[O-])[C@@H](O)[C@@H]1O	standard polar	2025-10-24	1769.97
Gas Chromatography	D-glucaro-1,5-lactone_TMS_2	C[Si](C)(C)O[C@@H]1[C@@H](C(=O)[O-])OC(=O)[C@H](O)[C@H]1O	standard polar	2025-10-24	1857.02
Gas Chromatography	D-glucaro-1,5-lactone_TMS_3	C[Si](C)(C)O[C@@H]1[C@@H](O)C(=O)O[C@H](C(=O)[O-])[C@H]1O	standard polar	2025-10-24	2432.88
Gas Chromatography	D-glucaro-1,5-lactone_TMS_4	C[Si](C)(C)O[C@@H]1[C@@H](C(=O)[O-])OC(=O)[C@H](O[Si](C)(C)C)[C@H]1O	standard polar	2025-10-24	1924.77
Gas Chromatography	D-glucaro-1,5-lactone_TMS_5	C[Si](C)(C)O[C@@H]1[C@@H](O[Si](C)(C)C)C(=O)O[C@H](C(=O)[O-])[C@H]1O	standard polar	2025-10-24	2447.64
Gas Chromatography	D-glucaro-1,5-lactone_TMS_6	C[Si](C)(C)O[C@@H]1[C@@H](C(=O)[O-])OC(=O)[C@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2391.59
Gas Chromatography	D-glucaro-1,5-lactone_TMS_7	C[Si](C)(C)O[C@@H]1[C@@H](O[Si](C)(C)C)C(=O)O[C@H](C(=O)[O-])[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2057.74

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	Proteobacteria	3

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

34448765

KEGG Compound ID

Not Available

BioCyc ID

CPD-12595

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46926210

PDB ID

Not Available

ChEBI ID

83384

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 D-glucaro-1,5-lactone (MMDBc0055864)

MOL for #<Metabolite:0x00007fadc4e744a0>

3D MOL for #<Metabolite:0x00007fadc4e744a0>

3D SDF for #<Metabolite:0x00007fadc4e744a0>

3D-SDF for #<Metabolite:0x00007fadc4e744a0>

PDB for #<Metabolite:0x00007fadc4e744a0>

3D PDB for #<Metabolite:0x00007fadc4e744a0>

SMILES for #<Metabolite:0x00007fadc4e744a0>

INCHI for #<Metabolite:0x00007fadc4e744a0>

Structure for #<Metabolite:0x00007fadc4e744a0>

3D Structure for #<Metabolite:0x00007fadc4e744a0>