MiMeDB: Showing metabocard for D-glucopyranuronate (MMDBc0056512)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-07-07 21:51:37 UTC

Update Date

2024-04-30 20:56:20 UTC

Metabolite ID

MMDBc0056512

Metabolite Identification

Common Name

D-glucopyranuronate

Description

D-glucopyranuronate, also known as glucuronate or glucuronic acid, belongs to the class of organic compounds known as glucuronic acid derivatives. Glucuronic acid derivatives are compounds containing a glucuronic acid moiety (or a derivative), which consists of a glucose moiety with the C6 carbon oxidized to a carboxylic acid. D-glucopyranuronate is an extremely weak basic (essentially neutral) compound (based on its pKa). D-glucopyranuronate exists in all living organisms, ranging from bacteria to humans. Outside of the human body, D-glucopyranuronate has been detected, but not quantified in, several different foods, such as horseradish tree, dandelions, peachs, almonds, and corns. This could make D-glucopyranuronate a potential biomarker for the consumption of these foods. A D-glucopyranuronate in cyclic pyranose form.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310111707472D          

 18 18  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  0  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
   -0.0000   -0.8250    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  1  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
 18  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056512

> <DATABASE_NAME>
MIME

> <SMILES>
[H]C1(O)O[C@]([H])(C(O)=O)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2-,3+,4-,6?/m0/s1

> <INCHI_KEY>
AEMOLEFTQBMNLQ-AQKNRBDQSA-N

> <FORMULA>
C6H10O7

> <MOLECULAR_WEIGHT>
194.1394

> <EXACT_MASS>
194.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.423258944666845

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S,5R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
-2.30

> <JCHEM_LOGP>
-2.61226468

> <ALOGPS_LOGS>
0.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.309229286068723

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2077910586517073

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6863365702254773

> <JCHEM_POLAR_SURFACE_AREA>
127.45

> <JCHEM_REFRACTIVITY>
35.7908

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.95e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-glucopyranuronic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-OCT-17         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+0
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
HETATM   18  H   UNK     0      -0.000  -1.540   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   18                                             
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                                                            
CONECT   18    6                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Value	Source
D-Glucuronic acid	ChEBI
Glucuronate	ChEBI
Glucuronic acid	ChEBI
D-Glucuronate	Generator
D-Glucopyranuronic acid	Generator
Glucuronate, monopotassium	MeSH
Glucuronic acid, monosodium salt	MeSH
Monopotassium glucuronate	MeSH
Glucuronate, monosodium	MeSH
Glucuronic acid, 6-(14)C-labeled, (D)-isomer	MeSH
Glucuronic acid, monopotassium salt	MeSH
Monosodium glucuronate	MeSH

Molecular Formula

C₆H₁₀O₇

Average Mass

194.1394

Monoisotopic Mass

194.042652674

IUPAC Name

(2S,3S,4S,5R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid

Traditional Name

D-glucopyranuronic acid

CAS Registry Number

Not Available

SMILES

[H]C1(O)O[C@]([H])(C(O)=O)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])O

InChI Identifier

InChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2-,3+,4-,6?/m0/s1

InChI Key

AEMOLEFTQBMNLQ-AQKNRBDQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glucuronic acid derivatives. Glucuronic acid derivatives are compounds containing a glucuronic acid moiety (or a derivative), which consists of a glucose moiety with the C6 carbon oxidized to a carboxylic acid.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glucuronic acid derivatives

Alternative Parents

Substituents

Glucuronic acid or derivatives
Beta-hydroxy acid
Hydroxy acid
Pyran
Monosaccharide
Oxane
Hemiacetal
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-glucuronic acid (CHEBI:47952 )
Uronic acids (C00191 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	295 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2.6	ChemAxon
logS	0.18	ALOGPS
pKa (Strongest Acidic)	3.21	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	127.45 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	35.79 m³·mol⁻¹	ChemAxon
Polarizability	16.42 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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a6s-5900000000-4d2f34d56893f9746201	2018-04-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-0900000000-580b96de2b78621ac645	2018-04-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-056s-1900000000-5b29218582cf3ee829fd	2018-04-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4r-9400000000-2aa876e0cbcc0ef3bddf	2018-04-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0007-0900000000-92dc7c30989ad23aad8e	2018-04-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0035-3900000000-e4373fb21fa3e097e6d0	2018-04-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9100000000-e6d71cf037c988640102	2018-04-06	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

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

HMDB0187523

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB006716

KNApSAcK ID

C00001123

Chemspider ID

Not Available

KEGG Compound ID

C00191

BioCyc ID

D-Glucopyranuronate

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

94715

PDB ID

Not Available

ChEBI ID

47952

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]

Showing metabocard for D-glucopyranuronate (MMDBc0056512)

MOL for #<Metabolite:0x00007feccb1f2330>

3D MOL for #<Metabolite:0x00007feccb1f2330>

3D SDF for #<Metabolite:0x00007feccb1f2330>

3D-SDF for #<Metabolite:0x00007feccb1f2330>

PDB for #<Metabolite:0x00007feccb1f2330>

3D PDB for #<Metabolite:0x00007feccb1f2330>

SMILES for #<Metabolite:0x00007feccb1f2330>

INCHI for #<Metabolite:0x00007feccb1f2330>

Structure for #<Metabolite:0x00007feccb1f2330>

3D Structure for #<Metabolite:0x00007feccb1f2330>