MiMeDB: Showing metabocard for L-arabinonate (MMDBc0056059)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:14:34 UTC

Update Date

2025-10-07 16:09:32 UTC

Metabolite ID

MMDBc0056059

Metabolite Identification

Common Name

L-arabinonate

Description

L-arabinonate is a dicarboxylic acid belonging to the class of sugar acids. Its chemical structure features a five-carbon backbone with two carboxyl groups, making it a key intermediate in various metabolic pathways. L-arabinonate is primarily involved in the Weimberg pathway, where it is converted by specific enzymes such as 2-keto-3-L-arabinonate dehydratase (L-KdpD) into α-ketoglutaric semialdehyde (KGSA), a crucial compound in amino acid biosynthesis and the citric acid cycle (PMID:32566996 ). The enzyme L-arabinonate dehydratase, identified in Rhizobium leguminosarum, is a large tetrameric protein that plays a significant role in the dehydration of L-arabinonate, and its structure includes a [2Fe-2S] cluster, which is essential for its catalytic activity (PMID:28574691 ). Mutations in the enzyme, such as the H579L variant, can alter substrate preferences, highlighting the enzyme's specificity and adaptability (PMID:39126499 ). Furthermore, the characterization of L-arabinonate dehydratase has implications for biotransformation processes that convert hemicellulose sugars into valuable chemicals (PMID:32566996 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222142D          

 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  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
    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  1  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  1  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>
MMDBc0056059

> <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+/m0/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-YVZJFKFKSA-M

> <FORMULA>
C5H9O6

> <MOLECULAR_WEIGHT>
165.122

> <EXACT_MASS>
165.04046159

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.948343024672619

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.7794093686666668

> <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

> <JCHEM_TRADITIONAL_IUPAC>
L-arabinonate

> <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       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
L-Arabinonic acid	Generator

Molecular Formula

C₅H₉O₆

Average Mass

165.122

Monoisotopic Mass

165.04046159

IUPAC Name

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

Traditional Name

L-arabinonate

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+/m0/s1

InChI Key

QXKAIJAYHKCRRA-YVZJFKFKSA-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

arabinonate (CHEBI:16501 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.8	ChemAxon
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	13.95 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

Not Available

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
Bacteria	Proteobacteria	1
Archaea/Archaea	Euryarchaeota	1
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

4573602

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5459849

PDB ID

Not Available

ChEBI ID

16501

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 L-arabinonate (MMDBc0056059)

MOL for #<Metabolite:0x00007fade9096ea8>

3D MOL for #<Metabolite:0x00007fade9096ea8>

3D SDF for #<Metabolite:0x00007fade9096ea8>

3D-SDF for #<Metabolite:0x00007fade9096ea8>

PDB for #<Metabolite:0x00007fade9096ea8>

3D PDB for #<Metabolite:0x00007fade9096ea8>

SMILES for #<Metabolite:0x00007fade9096ea8>

INCHI for #<Metabolite:0x00007fade9096ea8>

Structure for #<Metabolite:0x00007fade9096ea8>

3D Structure for #<Metabolite:0x00007fade9096ea8>