MiMeDB: Showing metabocard for L-Xylo-hexulonolactone (MMDBc0033134)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:36:07 UTC

Update Date

2022-08-31 22:26:35 UTC

Metabolite ID

MMDBc0033134

Metabolite Identification

Common Name

L-Xylo-hexulonolactone

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222372D          
 
 13 13  0  0  1  0            999 V2000
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -1.2695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -1.2695    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8974   -1.9370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6674   -0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8974   -1.9370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4521   -0.2300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819   -0.0724    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0964   -0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    0.7526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8109   -0.0724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -0.4849    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3819   -0.8974    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 12  1  1  0  0  0  0
  1  5  1  0  0  0  0
 12  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  3  6  1  1  0  0  0
  3  5  1  0  0  0  0
  5  7  2  0  0  0  0
 12  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  6  0  0  0
  9 11  1  0  0  0  0
 12 13  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033134

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,4-5,7-8,10H,1H2/t2-,4-,5+/m0/s1

> <INCHI_KEY>
PJBQWWHYTVYMLO-MDZRLIFHSA-N

> <FORMULA>
C6H8O6

> <MOLECULAR_WEIGHT>
176.1241

> <EXACT_MASS>
176.032087988

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
14.717534873807198

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,5R)-5-[(1S)-1,2-dihydroxyethyl]-3-hydroxyoxolane-2,4-dione

> <ALOGPS_LOGP>
-1.59

> <JCHEM_LOGP>
-1.977907794

> <ALOGPS_LOGS>
0.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.56966113107235

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.031665687731202

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9804889792565517

> <JCHEM_POLAR_SURFACE_AREA>
104.06

> <JCHEM_REFRACTIVITY>
34.087199999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.66e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-xylo-hex-3-ulonolactone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.770  -2.370   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -2.370   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.675  -3.616   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.246  -0.905   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.675  -3.616   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.711  -0.429   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.580  -0.135   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.913  -0.905   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.580   1.405   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -5.247  -0.135   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.246  -0.905   0.000  0.00  0.00           C+0
HETATM   13  H   UNK     0      -2.580  -1.675   0.000  0.00  0.00           H+0
CONECT    1   12    5                                                       
CONECT    2   12    3    4                                                  
CONECT    3    2    6    5                                                  
CONECT    4    2                                                            
CONECT    5    1    3    7                                                  
CONECT    6    3                                                            
CONECT    7    5                                                            
CONECT    8   12    9   10                                                  
CONECT    9    8   11                                                       
CONECT   10    8                                                            
CONECT   11    9                                                            
CONECT   12    1    2    8   13                                             
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

Synonyms

Not Available

Molecular Formula

C₆H₈O₆

Average Mass

176.1241

Monoisotopic Mass

176.032087988

IUPAC Name

(3S,5R)-5-[(1S)-1,2-dihydroxyethyl]-3-hydroxyoxolane-2,4-dione

Traditional Name

L-xylo-hex-3-ulonolactone

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,4-5,7-8,10H,1H2/t2-,4-,5+/m0/s1

InChI Key

PJBQWWHYTVYMLO-MDZRLIFHSA-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

3-furanone
Gamma butyrolactone
1,3-dicarbonyl compound
Tetrahydrofuran
Carboxylic acid ester
Ketone
Secondary alcohol
Cyclic ketone
Monocarboxylic acid or derivatives
Oxacycle
Carboxylic acid derivative
Primary alcohol
Organooxygen compound
Organic oxide
Organic oxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

ketoaldonolactone (CHEBI:28745 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	466 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-2	ChemAxon
logS	0.42	ALOGPS
pKa (Strongest Acidic)	8.03	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.06 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	34.09 m³·mol⁻¹	ChemAxon
Polarizability	14.72 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	splash10-0ab9-9300000000-12edc9e854b5d3fb3586	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-056r-1900000000-e1a2060288dfa69a7ec8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0bvl-4900000000-74e70c33e8c3508563fa	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9100000000-1d099791076040e7718b	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-02di-2900000000-fa7a82a4c6641c430ce9	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0bvi-4900000000-98c1a460a58345baee05	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-08fu-9300000000-e00125e18c3f7a734652	2016-09-12	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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
MMDBr0008397	Ascorbic acid	L-Xylo-hexulonolactone	Not Available		VMH	30371894
MMDBr0008398	L-Gulono-1,4-lactone	Hydrogen peroxide	Not Available		VMH	30371894

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown
Bacteria	Firmicutes	10	Human ; Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	17	Human feces; Human	Metabolic reconstruction

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

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

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5461125

PDB ID

Not Available

ChEBI ID

28745

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for L-Xylo-hexulonolactone (MMDBc0033134)

MOL for #<Metabolite:0x00007fdb58dad4d8>

3D MOL for #<Metabolite:0x00007fdb58dad4d8>

3D SDF for #<Metabolite:0x00007fdb58dad4d8>

3D-SDF for #<Metabolite:0x00007fdb58dad4d8>

PDB for #<Metabolite:0x00007fdb58dad4d8>

3D PDB for #<Metabolite:0x00007fdb58dad4d8>

SMILES for #<Metabolite:0x00007fdb58dad4d8>

INCHI for #<Metabolite:0x00007fdb58dad4d8>

Structure for #<Metabolite:0x00007fdb58dad4d8>

3D Structure for #<Metabolite:0x00007fdb58dad4d8>