MiMeDB: Showing metabocard for (3R)-hydroxybutanoic acid dimer (MMDBc0054907)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:37:37 UTC

Update Date

2025-10-07 16:08:46 UTC

Metabolite ID

MMDBc0054907

Metabolite Identification

Common Name

(3R)-hydroxybutanoic acid dimer

Description

(3R)-hydroxybutanoic acid dimer is a dimeric form of a hydroxy acid, specifically belonging to the class of organic compounds known as carboxylic acids. There is little literature available on this metabolite, indicating a gap in research regarding its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221372D          

 15 14  0  0  1  0            999 V2000
    1.3480   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6349   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.3493   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4914   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0638   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3493   -1.5395    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.4914   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2059   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.1105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6349   -1.1270    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  1  0  0  0
  6  4  1  0  0  0  0
  7  4  1  0  0  0  0
  8  3  1  0  0  0  0
  5  9  1  1  0  0  0
 10  7  2  0  0  0  0
 11  7  1  0  0  0  0
 12  8  2  0  0  0  0
 13  6  1  0  0  0  0
 13  8  1  0  0  0  0
  5 14  1  1  0  0  0
  6 15  1  6  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0054907

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H14O5/c1-5(9)3-8(12)13-6(2)4-7(10)11/h5-6,9H,3-4H2,1-2H3,(H,10,11)/p-1/t5-,6-/m1/s1

> <INCHI_KEY>
RILHUWWTCSDPAN-PHDIDXHHSA-M

> <FORMULA>
C8H13O5

> <MOLECULAR_WEIGHT>
189.188

> <EXACT_MASS>
189.076847099

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
18.304417365167225

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-3-{[(3R)-3-hydroxybutanoyl]oxy}butanoate

> <JCHEM_LOGP>
-0.1095408740000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.407217281495427

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.225095081503412

> <JCHEM_PKA_STRONGEST_BASIC>
-2.620683437930942

> <JCHEM_POLAR_SURFACE_AREA>
86.66000000000001

> <JCHEM_REFRACTIVITY>
54.27310000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-{[(3R)-3-hydroxybutanoyl]oxy}butanoate

> <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       2.516  -0.564   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.185  -2.874   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.518  -0.564   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.185  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.852  -1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.517  -1.334   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.850  -2.874   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      13.186  -0.564   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      11.852  -2.874   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       6.517  -2.874   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       7.851  -0.564   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       3.850   0.206   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0      10.518  -2.104   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    5    8                                                       
CONECT    4    6    7                                                       
CONECT    5    1    3    9   14                                             
CONECT    6    2    4   13   15                                             
CONECT    7    4   10   11                                                  
CONECT    8    3   12   13                                                  
CONECT    9    5                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    8                                                            
CONECT   13    6    8                                                       
CONECT   14    5                                                            
CONECT   15    6                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
(3R)-Hydroxybutanoate dimer	ChEBI
(R)-3-((R)-3-Hydroxybutanoyloxy)butanoate	ChEBI
(3R)-Hydroxybutanoic acid dimer	Generator
(R)-3-((R)-3-Hydroxybutanoyloxy)butanoic acid	Generator

Molecular Formula

C₈H₁₃O₅

Average Mass

189.188

Monoisotopic Mass

189.076847099

IUPAC Name

(3R)-3-{[(3R)-3-hydroxybutanoyl]oxy}butanoate

Traditional Name

(3R)-3-{[(3R)-3-hydroxybutanoyl]oxy}butanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C8H14O5/c1-5(9)3-8(12)13-6(2)4-7(10)11/h5-6,9H,3-4H2,1-2H3,(H,10,11)/p-1/t5-,6-/m1/s1

InChI Key

RILHUWWTCSDPAN-PHDIDXHHSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Beta hydroxy acids and derivatives

Direct Parent

Beta hydroxy acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Fatty acid ester
Dicarboxylic acid or derivatives
Fatty acyl
Secondary alcohol
Carboxylic acid ester
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

hydroxy monocarboxylic acid anion (CHEBI:10979 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-0.11	ChemAxon
pKa (Strongest Acidic)	4.23	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	86.66 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	54.27 m³·mol⁻¹	ChemAxon
Polarizability	18.3 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	76.0
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	28.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	353.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	485.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	351.1
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	303.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	1638.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	76.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	794.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	314.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	206.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	174.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	101.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	177.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	561.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	63.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	278.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1227.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	777.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(3R)-hydroxybutanoic acid dimer_TMS_1	C[C@H](CC(=O)[O-])OC(=O)C[C@@H](C)O[Si](C)(C)C	standard non polar	2025-10-24	2183.48
Gas Chromatography	(3R)-hydroxybutanoic acid dimer_TMS_1	C[C@H](CC(=O)[O-])OC(=O)C[C@@H](C)O[Si](C)(C)C	standard polar	2025-10-24	1888.72

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	26	Human ; Human feces

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

7827646

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9548723

PDB ID

Not Available

ChEBI ID

10979

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 (3R)-hydroxybutanoic acid dimer (MMDBc0054907)

MOL for #<Metabolite:0x00007f9acc750558>

3D MOL for #<Metabolite:0x00007f9acc750558>

3D SDF for #<Metabolite:0x00007f9acc750558>

3D-SDF for #<Metabolite:0x00007f9acc750558>

PDB for #<Metabolite:0x00007f9acc750558>

3D PDB for #<Metabolite:0x00007f9acc750558>

SMILES for #<Metabolite:0x00007f9acc750558>

INCHI for #<Metabolite:0x00007f9acc750558>

Structure for #<Metabolite:0x00007f9acc750558>

3D Structure for #<Metabolite:0x00007f9acc750558>