Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2023-02-21 17:14:48 UTC

HMDB ID

HMDB0000409

Secondary Accession Numbers

HMDB00409

Metabolite Identification

Common Name

(5R)-5-Hydroxyhexanoic acid

Description

(5R)-5-Hydroxyhexanoic acid, also known as (5R)-5-hydroxycaproate or HMBA, belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. Based on a literature review very few articles have been published on (5R)-5-Hydroxyhexanoic acid.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(-)-5-Hydroxycaproic acid	ChEBI
(-)-5-Hydroxyhexanoic acid	ChEBI
(5R)-5-Hydroxycaproic acid	ChEBI
(R)-(-)-5-Hydroxyhexanoic acid	ChEBI
(-)-5-Hydroxycaproate	Generator
(-)-5-Hydroxyhexanoate	Generator
(5R)-5-Hydroxycaproate	Generator
(R)-(-)-5-Hydroxyhexanoate	Generator
(5R)-5-Hydroxyhexanoate	Generator
(5R)-5-Hydroxy-hexanoate	HMDB
(5R)-5-Hydroxy-hexanoic acid	HMDB
HMBA	HMDB
5R-Hydroxy-hexanoate	HMDB

Chemical Formula

C₆H₁₂O₃

Average Molecular Weight

132.1577

Monoisotopic Molecular Weight

132.07864425

IUPAC Name

(5R)-5-hydroxyhexanoic acid

Traditional Name

HMBA

CAS Registry Number

83972-61-6

SMILES

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

InChI Identifier

InChI=1S/C6H12O3/c1-5(7)3-2-4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m1/s1

InChI Key

YDCRNMJQROAWFT-RXMQYKEDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Hydroxy fatty acid
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

medium-chain fatty acid (CHEBI:78842 )
(omega-1)-hydroxy fatty acid (CHEBI:78842 )
Hydroxy fatty acids (LMFA01050376 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0000409)
Cell membrane (HMDB: HMDB0000409)

Organelle

Adiposome (HMDB: HMDB0000409)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0000409)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0000409)

Source

Endogenous

Endogenous (HMDB: HMDB0000409)

Animal

Animal (HMDB: HMDB0000409)

Exogenous

Food

Food (HMDB: HMDB0000409)

Animal origin

Poultry

Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)
Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)

Equine

Horse (FooDB: FOOD00378)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0000409)

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0000409)

Biochemical process

Lipid transport (HMDB: HMDB0000409)

Role

Biological role

Energy storage (HMDB: HMDB0000409)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	128 g/L	ALOGPS
logP	0.32	ALOGPS
logP	0.35	ChemAxon
logS	-0.02	ALOGPS
pKa (Strongest Acidic)	4.71	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	32.82 m³·mol⁻¹	ChemAxon
Polarizability	14.02 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	128.332	31661259
DarkChem	[M-H]-	125.177	31661259
AllCCS	[M+H]+	131.823	32859911
AllCCS	[M-H]-	129.325	32859911
DeepCCS	[M+H]+	128.209	30932474
DeepCCS	[M-H]-	124.489	30932474
DeepCCS	[M-2H]-	161.32	30932474
DeepCCS	[M+Na]+	136.772	30932474
AllCCS	[M+H]+	131.8	32859911
AllCCS	[M+H-H2O]+	127.7	32859911
AllCCS	[M+NH4]+	135.7	32859911
AllCCS	[M+Na]+	136.8	32859911
AllCCS	[M-H]-	129.3	32859911
AllCCS	[M+Na-2H]-	132.0	32859911
AllCCS	[M+HCOO]-	135.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(5R)-5-Hydroxyhexanoic acid	C[C@@H](O)CCCC(O)=O	2439.1	Standard polar	33892256
(5R)-5-Hydroxyhexanoic acid	C[C@@H](O)CCCC(O)=O	1149.7	Standard non polar	33892256
(5R)-5-Hydroxyhexanoic acid	C[C@@H](O)CCCC(O)=O	1185.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(5R)-5-Hydroxyhexanoic acid,1TMS,isomer #1	C[C@H](CCCC(=O)O)O[Si](C)(C)C	1284.7	Semi standard non polar	33892256
(5R)-5-Hydroxyhexanoic acid,1TMS,isomer #2	C[C@@H](O)CCCC(=O)O[Si](C)(C)C	1260.3	Semi standard non polar	33892256
(5R)-5-Hydroxyhexanoic acid,2TMS,isomer #1	C[C@H](CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	1361.3	Semi standard non polar	33892256
(5R)-5-Hydroxyhexanoic acid,1TBDMS,isomer #1	C[C@H](CCCC(=O)O)O[Si](C)(C)C(C)(C)C	1532.3	Semi standard non polar	33892256
(5R)-5-Hydroxyhexanoic acid,1TBDMS,isomer #2	C[C@@H](O)CCCC(=O)O[Si](C)(C)C(C)(C)C	1479.5	Semi standard non polar	33892256
(5R)-5-Hydroxyhexanoic acid,2TBDMS,isomer #1	C[C@H](CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	1812.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (5R)-5-Hydroxyhexanoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0077-9100000000-13a584fc9ff05431f359	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R)-5-Hydroxyhexanoic acid GC-MS (2 TMS) - 70eV, Positive	splash10-007c-9420000000-7b0146069089183f6082	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R)-5-Hydroxyhexanoic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R)-5-Hydroxyhexanoic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R)-5-Hydroxyhexanoic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R)-5-Hydroxyhexanoic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R)-5-Hydroxyhexanoic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R)-5-Hydroxyhexanoic acid GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 10V, Positive-QTOF	splash10-014j-5900000000-3bf905a3ced857b422b1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 20V, Positive-QTOF	splash10-014i-9400000000-b18891bb2981129af001	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 40V, Positive-QTOF	splash10-066r-9000000000-3510777085e9e83a6561	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 10V, Negative-QTOF	splash10-001i-2900000000-3b9f578bc70674738913	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 20V, Negative-QTOF	splash10-03e9-4900000000-9944af827f01e265b301	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 40V, Negative-QTOF	splash10-0a4l-9000000000-9f3f80d6749af1cc6dbb	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 10V, Negative-QTOF	splash10-03ei-3900000000-49a5b195fc6d1869f127	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 20V, Negative-QTOF	splash10-0bta-9400000000-9da83e480e59bbc1ade7	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 40V, Negative-QTOF	splash10-052g-9000000000-e9748f05fe518d153135	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 10V, Positive-QTOF	splash10-014j-9400000000-744ecd7d7e40b1357594	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 20V, Positive-QTOF	splash10-05tk-9000000000-086484b097d1ba55d5d0	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R)-5-Hydroxyhexanoic acid 40V, Positive-QTOF	splash10-052f-9000000000-db58a877cf5945d523f9	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022025

KNApSAcK ID

Not Available

Chemspider ID

5474600

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5398

PubChem Compound

7131043

PDB ID

Not Available

ChEBI ID

78842

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Fazio, Fabio; Schneider, Manfred P. FA-catalyzed trimerization of R-(+)-6-methyltetrahydro-2-pyranone. FB 9-Bergische Universitat-GH-Wuppertal, Wuppertal, Germany. Tetrahedron Letters (2002), 43(5), 811-814.

Material Safety Data Sheet (MSDS)

Not Available

General References

Kamerling JP, Duran M, Bruinvis L, Ketting D, Wadman SK, Vliegenthart JF: The absolute configuration of urinary 5-hydroxyhexanoic acid - a product of fatty acid (omega-1)-oxidation - in patients with non-ketotic dicarboxylic aciduria. Clin Chim Acta. 1982 Nov 10;125(3):247-54. [PubMed:6897376 ]

Showing metabocard for (5R)-5-Hydroxyhexanoic acid (HMDB0000409)

MOL for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

3D MOL for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

3D SDF for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

3D-SDF for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

PDB for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

3D PDB for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

SMILES for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

INCHI for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

Structure for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

3D Structure for HMDB0000409 ((5R)-5-Hydroxyhexanoic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra