MiMeDB: Showing metabocard for D-fuconic acid (MMDBc0055861)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:01 UTC

Update Date

2025-10-07 16:09:25 UTC

Metabolite ID

MMDBc0055861

Metabolite Identification

Common Name

D-fuconic acid

Description

D-fuconic acid is a carbohydrate derivative belonging to the class of aldonic acids. Its chemical structure features a six-carbon backbone with a carboxylic acid functional group, which is characteristic of aldonic acids. D-fuconic acid is involved in various biochemical pathways, particularly as a substrate for specific enzymes that facilitate its conversion into other metabolites. For instance, studies have shown that it can form protein complexes, as evidenced by the successful crystallization of proteins bound to d-fuconic acid alongside other aldonic acids (PMID:33630388 ). Furthermore, thermal shift assays have demonstrated its interaction with proteins, revealing a dissociation constant (KD) of 13.50 ± 1.6 µM, indicating its binding affinity in biochemical contexts (PMID:28407382 ). The structural data for d-fuconic acid can be accessed in the Protein Data Bank, highlighting its relevance in structural biology and metabolic studies (PMID:33630388 ). Overall, D-fuconic acid serves as an important metabolite within carbohydrate metabolism, contributing to various enzymatic reactions and protein interactions.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222092D          

 16 15  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  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
    2.4750    0.6039    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
    2.4750    2.2539    0.0000 H   0  0  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  5  1  0  0  0  0
  2  7  1  1  0  0  0
  3  8  1  1  0  0  0
  4  9  1  6  0  0  0
  5 10  1  6  0  0  0
 11  6  2  0  0  0  0
 12  6  1  0  0  0  0
  2 13  1  1  0  0  0
  3 14  1  1  0  0  0
  4 15  1  6  0  0  0
  5 16  1  6  0  0  0
M  CHG  1  12  -1
M  END
> <DATABASE_ID>
MMDBc0055861

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O6/c1-2(7)3(8)4(9)5(10)6(11)12/h2-5,7-10H,1H3,(H,11,12)/p-1/t2-,3+,4+,5-/m1/s1

> <INCHI_KEY>
NBFWIISVIFCMDK-MGCNEYSASA-M

> <FORMULA>
C6H11O6

> <MOLECULAR_WEIGHT>
179.149

> <EXACT_MASS>
179.056111654

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.705525281018883

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.362834344

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.704809226791319

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.533365129686107

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0491138226804058

> <JCHEM_POLAR_SURFACE_AREA>
121.05000000000001

> <JCHEM_REFRACTIVITY>
47.5644

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
D-fuconate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O-1
HETATM   13  H   UNK     0       4.620   4.207   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       7.287   4.207   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       8.621   1.897   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    7   13                                             
CONECT    3    2    4    8   14                                             
CONECT    4    3    5    9   15                                             
CONECT    5    4    6   10   16                                             
CONECT    6    5   11   12                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    6                                                            
CONECT   13    2                                                            
CONECT   14    3                                                            
CONECT   15    4                                                            
CONECT   16    5                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
D-Fuconic acid	Generator

Molecular Formula

C₆H₁₁O₆

Average Mass

179.149

Monoisotopic Mass

179.056111654

IUPAC Name

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

Traditional Name

D-fuconate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H12O6/c1-2(7)3(8)4(9)5(10)6(11)12/h2-5,7-10H,1H3,(H,11,12)/p-1/t2-,3+,4+,5-/m1/s1

InChI Key

NBFWIISVIFCMDK-MGCNEYSASA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Sugar acid
Fatty acyl
Fatty acid
Monosaccharide
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Polyol
Monocarboxylic acid or derivatives
Alcohol
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

fuconate (CHEBI:35372 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.4	ChemAxon
pKa (Strongest Acidic)	3.53	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	47.56 m³·mol⁻¹	ChemAxon
Polarizability	15.71 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, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	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	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

5256738

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6857398

PDB ID

Not Available

ChEBI ID

35372

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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-fuconic acid (MMDBc0055861)

MOL for #<Metabolite:0x00007fadcc31d108>

3D MOL for #<Metabolite:0x00007fadcc31d108>

3D SDF for #<Metabolite:0x00007fadcc31d108>

3D-SDF for #<Metabolite:0x00007fadcc31d108>

PDB for #<Metabolite:0x00007fadcc31d108>

3D PDB for #<Metabolite:0x00007fadcc31d108>

SMILES for #<Metabolite:0x00007fadcc31d108>

INCHI for #<Metabolite:0x00007fadcc31d108>

Structure for #<Metabolite:0x00007fadcc31d108>

3D Structure for #<Metabolite:0x00007fadcc31d108>