MiMeDB: Showing metabocard for D-galactaro-1,5-lactone (MMDBc0054427)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:11:56 UTC

Update Date

2022-08-12 20:09:00 UTC

Metabolite ID

MMDBc0054427

Metabolite Identification

Common Name

D-galactaro-1,5-lactone

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05031419352D          

 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  2  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
    1.1468    1.6002    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  5  1  6  0  0  0
  6  3  1  0  0  0  0
  1  7  1  6  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  1  0  0  0
  2 15  1  1  0  0  0
  3 16  1  6  0  0  0
  4 17  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054427

> <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)/t1-,2+,3+,4-/m0/s1

> <INCHI_KEY>
YLKFQNUGXOLRNI-KXMYSMCESA-N

> <FORMULA>
C6H8O7

> <MOLECULAR_WEIGHT>
192.1235

> <EXACT_MASS>
192.02700261

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
15.504313668057318

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.03

> <JCHEM_LOGP>
-2.4249986480000003

> <ALOGPS_LOGS>
-0.05

> <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>
124.29

> <JCHEM_REFRACTIVITY>
34.6462

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.72e+02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       0.000   0.000   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
(2S,3R,4S,5R)-3,4,5-Trihydroxy-6-oxotetrahydro-2H-pyran-2-carboxylic acid	ChEBI
1,5-Galactarolactone	ChEBI
Galactaro-1,5-lactone	ChEBI
Galactarolactone	ChEBI
(2S,3R,4S,5R)-3,4,5-Trihydroxy-6-oxotetrahydro-2H-pyran-2-carboxylate	Generator

Molecular Formula

C₆H₈O₇

Average Mass

192.1235

Monoisotopic Mass

192.02700261

IUPAC Name

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

Traditional Name

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

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)/t1-,2+,3+,4-/m0/s1

InChI Key

YLKFQNUGXOLRNI-KXMYSMCESA-N

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
Oxane
Pyran
Lactone
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Polyol
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

carbohydrate acid (CHEBI:84190 )
aldarolactone (CHEBI:84190 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	172 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.4	ChemAxon
logS	-0.05	ALOGPS
pKa (Strongest Acidic)	3.05	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	1	ChemAxon
Refractivity	34.65 m³·mol⁻¹	ChemAxon
Polarizability	15.5 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 (TMS_2_3) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004l-0900000000-80f3c91cb6dda7129476	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-056r-1900000000-c2e587105e58d19ba39f	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4u-9300000000-56d972f71b244bf06586	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0007-0900000000-f96cf52b61d20d73ee52	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-006w-3900000000-f2282a7e4e22cfa976a1	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-48e95b30921e00f146d8	2019-02-23	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	3

Exposure Sources

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CPD-17138

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53321658

PDB ID

Not Available

ChEBI ID

84190

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-galactaro-1,5-lactone (MMDBc0054427)

MOL for #<Metabolite:0x00007fdb71803410>

3D MOL for #<Metabolite:0x00007fdb71803410>

3D SDF for #<Metabolite:0x00007fdb71803410>

3D-SDF for #<Metabolite:0x00007fdb71803410>

PDB for #<Metabolite:0x00007fdb71803410>

3D PDB for #<Metabolite:0x00007fdb71803410>

SMILES for #<Metabolite:0x00007fdb71803410>

INCHI for #<Metabolite:0x00007fdb71803410>

Structure for #<Metabolite:0x00007fdb71803410>

3D Structure for #<Metabolite:0x00007fdb71803410>