MiMeDB: Showing metabocard for D-xylonate (MMDBc0054443)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:12:31 UTC

Update Date

2025-10-07 16:04:11 UTC

Metabolite ID

MMDBc0054443

Metabolite Identification

Common Name

D-xylonate

Description

D-xylonate is a dicarboxylic acid and a key metabolite in various biochemical pathways. Its chemical structure features a five-carbon backbone with two carboxyl groups, making it a member of the dicarboxylic acid class. D-xylonate plays a significant role in microbial metabolism, particularly in the Weimberg pathway, where it is involved in the conversion of d-xylose to valuable products. However, the low catalytic activity of d-xylonate dehydratase, crucial for the production of d-1,2,4-butanetriol from d-xylose, leads to the accumulation of d-xylonic acid, presenting a bottleneck in this metabolic route (PMID:40747351 ). Efforts to enhance the activity of d-xylonate dehydratase through enzyme engineering and modification of the iron-sulfur cluster synthesis system have been explored (PMID:40747351 ). Additionally, d-xylonate accumulation in microbial cultures has been linked to inefficiencies in hydrolysis and uptake processes, prompting research into overexpressing transporter genes to improve its utilization (PMID:39021639 ). Overall, d-xylonate is integral to various metabolic pathways, influencing both microbial growth and the production of biochemicals.

Structure

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


  Mrv1652308272122232D          

 14 13  0  0  1  0            999 V2000
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  2  7  1  6  0  0  0
  3  8  1  6  0  0  0
  4  9  1  6  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
  2 12  1  6  0  0  0
  3 13  1  6  0  0  0
  4 14  1  6  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0054443

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/p-1/t2-,3+,4-/m1/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-FLRLBIABSA-M

> <FORMULA>
C5H9O6

> <MOLECULAR_WEIGHT>
165.122

> <EXACT_MASS>
165.04046159

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.888888653633074

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R)-2,3,4,5-tetrahydroxypentanoate

> <ALOGPS_LOGP>
-1.92

> <JCHEM_LOGP>
-2.7794093686666668

> <ALOGPS_LOGS>
0.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.768659694136133

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.393139811550542

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974562302797298

> <JCHEM_POLAR_SURFACE_AREA>
121.05000000000001

> <JCHEM_REFRACTIVITY>
43.145599999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.57e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-xylonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-AUG-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-AUG-21         0                                  
HETATM    1  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O-1
HETATM   12  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       7.287   4.207   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       8.621   1.897   0.000  0.00  0.00           H+0
CONECT    1    2    6                                                       
CONECT    2    1    3    7   12                                             
CONECT    3    2    4    8   13                                             
CONECT    4    3    5    9   14                                             
CONECT    5    4   10   11                                                  
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    2                                                            
CONECT   13    3                                                            
CONECT   14    4                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
D-Xylonic acid	Generator

Molecular Formula

C₅H₉O₆

Average Mass

165.122

Monoisotopic Mass

165.04046159

IUPAC Name

(2R,3S,4R)-2,3,4,5-tetrahydroxypentanoate

Traditional Name

D-xylonate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/p-1/t2-,3+,4-/m1/s1

InChI Key

QXKAIJAYHKCRRA-FLRLBIABSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Pentose monosaccharide
Beta-hydroxy acid
Short-chain hydroxy acid
Sugar acid
Monosaccharide
Hydroxy acid
Fatty acid
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Alcohol
Primary alcohol
Organic oxide
Carbonyl group
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

xylonate (CHEBI:17746 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	857 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-2.8	ChemAxon
logS	0.67	ALOGPS
pKa (Strongest Acidic)	3.39	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	121.05 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	43.15 m³·mol⁻¹	ChemAxon
Polarizability	13.89 Å³	ChemAxon
Number of Rings	0	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, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

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
Archaea/Archaea	Euryarchaeota	1
Bacteria/Eubacteria	Proteobacteria	1
Bacteria	Proteobacteria	1

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

HMDB0242170

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4573736

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Xylonic acid

METLIN ID

Not Available

PubChem Compound

5460056

PDB ID

Not Available

ChEBI ID

17746

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Kong SW, Hernandez-Ferrer C: Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020;25:587-598. [PubMed:31797630 ]

Showing metabocard for D-xylonate (MMDBc0054443)

MOL for #<Metabolite:0x00007fade01af578>

3D MOL for #<Metabolite:0x00007fade01af578>

3D SDF for #<Metabolite:0x00007fade01af578>

3D-SDF for #<Metabolite:0x00007fade01af578>

PDB for #<Metabolite:0x00007fade01af578>

3D PDB for #<Metabolite:0x00007fade01af578>

SMILES for #<Metabolite:0x00007fade01af578>

INCHI for #<Metabolite:0x00007fade01af578>

Structure for #<Metabolite:0x00007fade01af578>

3D Structure for #<Metabolite:0x00007fade01af578>