MiMeDB: Showing metabocard for D-glucaro-1,4-lactone (MMDBc0054432)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:12:02 UTC

Update Date

2022-08-12 20:09:00 UTC

Metabolite ID

MMDBc0054432

Metabolite Identification

Common Name

D-glucaro-1,4-lactone

Description

D-Glucaro-1,4-lactone, also known as D-saccharolactone or 1,4-D-glucarolactone, belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. D-Glucaro-1,4-lactone has been detected, but not quantified in, several different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), domestic pigs (Sus scrofa domestica), and milk (cow). This could make D-glucaro-1,4-lactone a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on D-Glucaro-1,4-lactone.

Structure

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


  Mrv1652304032018422D          

 17 17  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1296   -1.5764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6145   -2.2438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3091   -1.6626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778    1.4392    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1304    1.7177    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6447   -0.9089    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7951   -0.0262    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  1  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  1  7  1  1  0  0  0
  2  8  1  6  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  6  0  0  0
  2 15  1  1  0  0  0
  3 16  1  1  0  0  0
  4 17  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054432

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O7/c7-1-2(8)6(12)13-4(1)3(9)5(10)11/h1-4,7-9H,(H,10,11)/t1-,2-,3+,4+/m1/s1

> <INCHI_KEY>
XECPAIJNBXCOBO-MMPJQOAZSA-N

> <FORMULA>
C6H8O7

> <MOLECULAR_WEIGHT>
192.1235

> <EXACT_MASS>
192.02700261

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
15.621192243530285

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-[(2S,3R,4R)-3,4-dihydroxy-5-oxooxolan-2-yl]-2-hydroxyacetic acid

> <ALOGPS_LOGP>
-1.89

> <JCHEM_LOGP>
-2.4249986480000003

> <ALOGPS_LOGS>
-0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.622577499257503

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0635792127453407

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7457384752052727

> <JCHEM_POLAR_SURFACE_AREA>
124.29

> <JCHEM_REFRACTIVITY>
34.6462

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-[(2S,3R,4R)-3,4-dihydroxy-5-oxooxolan-2-yl](hydroxy)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-APR-20         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.109  -2.943   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.267  -1.375   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.014  -4.188   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.577  -3.104   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.290  -0.290   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       2.012   2.687   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       2.110   3.206   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       1.203  -1.697   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       3.351  -0.049   0.000  0.00  0.00           H+0
CONECT    1    2    4    7   14                                             
CONECT    2    1    6    8   15                                             
CONECT    3    4    5    9   16                                             
CONECT    4    1    3   13   17                                             
CONECT    5    3   10   11                                                  
CONECT    6    2   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
1,4-D-Glucarolactone	ChEBI
1,4-Glucarolactone	ChEBI
D-Saccharolactone	ChEBI
Saccharolactone	ChEBI
Saccharolactone, monocalcium salt, (D)-isomer	HMDB
Saccharolactone, (D)-isomer	HMDB
Saccharolactone, monosodium salt, (D)-isomer	HMDB
Glucarate-1,4-lactone	HMDB

Molecular Formula

C₆H₈O₇

Average Mass

192.1235

Monoisotopic Mass

192.02700261

IUPAC Name

(2S)-2-[(2S,3R,4R)-3,4-dihydroxy-5-oxooxolan-2-yl]-2-hydroxyacetic acid

Traditional Name

(S)-[(2S,3R,4R)-3,4-dihydroxy-5-oxooxolan-2-yl](hydroxy)acetic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H8O7/c7-1-2(8)6(12)13-4(1)3(9)5(10)11/h1-4,7-9H,(H,10,11)/t1-,2-,3+,4+/m1/s1

InChI Key

XECPAIJNBXCOBO-MMPJQOAZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Gamma butyrolactones

Direct Parent

Gamma butyrolactones

Alternative Parents

Substituents

Alpha-hydroxy acid
Dicarboxylic acid or derivatives
Gamma butyrolactone
Hydroxy acid
Tetrahydrofuran
Secondary alcohol
Carboxylic acid ester
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

delta-lactone (CHEBI:85805 )
aldarolactone (CHEBI:85805 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	159 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-2.4	ChemAxon
logS	-0.08	ALOGPS
pKa (Strongest Acidic)	3.06	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	124.29 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	34.65 m³·mol⁻¹	ChemAxon
Polarizability	15.62 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	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-014i-1971000000-6bc480f6132ff3b4f3a8	2014-06-16	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-08i9-9300000000-3036b01985ecba9285d8	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-01di-6258900000-672b193020e251e41668	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 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	splash10-004l-1900000000-2ec6e385ad66bb32dbf6	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-05r1-2900000000-8b979b3c9f43a65b913f	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00du-9000000000-6d6b84a7185d89c6f912	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00tg-4900000000-21eb31d409626b01009c	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-016s-2900000000-f8f32d204349bf201366	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0603-9300000000-96973bb25faba1a35f09	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-cc5bb18d1664b93a313a	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00os-6900000000-1ba0094376fd3554d23c	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ox-9000000000-ca8224ed70a4c6b3efbe	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00bc-6900000000-b6467151416eacaa1e10	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9100000000-2c5aa67ce4b96aaedd10	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6u-9000000000-fe8344a8a3a320b12c81	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	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

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	Proteobacteria	1

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

HMDB0041862

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB098184

KNApSAcK ID

Not Available

Chemspider ID

109061

KEGG Compound ID

Not Available

BioCyc ID

CPD-17141

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

122306

PDB ID

Not Available

ChEBI ID

85805

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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-1,4-lactone (MMDBc0054432)

MOL for #<Metabolite:0x00005634c2b8ac70>

3D MOL for #<Metabolite:0x00005634c2b8ac70>

3D SDF for #<Metabolite:0x00005634c2b8ac70>

3D-SDF for #<Metabolite:0x00005634c2b8ac70>

PDB for #<Metabolite:0x00005634c2b8ac70>

3D PDB for #<Metabolite:0x00005634c2b8ac70>

SMILES for #<Metabolite:0x00005634c2b8ac70>

INCHI for #<Metabolite:0x00005634c2b8ac70>

Structure for #<Metabolite:0x00005634c2b8ac70>

3D Structure for #<Metabolite:0x00005634c2b8ac70>