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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

2021-09-14 15:40:00 UTC

HMDB ID

HMDB0000642

Secondary Accession Numbers

HMDB00642

Metabolite Identification

Common Name

Erythronilic acid

Description

Erythronilic acid, also known as (2R,3S)-3-hydroxy-2-methylbutanoic acid (HMBA), is a normal urinary metabolite involved in isoleucine catabolism, beta-oxidation of fatty acids, and ketogenesis. HMDB is excreted in abnormally high amounts in beta-ketothiolase deficiency. Differences in the enantiomeric ratio of HMBA may originate from the enantioselectivity of different enzyme systems (PMID: 10755375 ).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Erythronilate	Generator
(-)-Erythro-nilic acid	HMDB
(2R,3S)-3-Hydroxy-2-methylbutanoic acid	HMDB
(2R,3S)-3-Hydroxy-2-methylbutyric acid	HMDB
HMBA	HMDB
Erythronilic acid	HMDB

Chemical Formula

C₅H₁₀O₃

Average Molecular Weight

118.1311

Monoisotopic Molecular Weight

118.062994186

IUPAC Name

(2R,3S)-3-hydroxy-2-methylbutanoic acid

Traditional Name

erythronilate

CAS Registry Number

66729-02-0

SMILES

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

InChI Identifier

InChI=1S/C5H10O3/c1-3(4(2)6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t3-,4+/m1/s1

InChI Key

VEXDRERIMPLZLU-DMTCNVIQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Beta-hydroxy acid
Branched fatty acid
Hydroxy fatty acid
Short-chain hydroxy acid
Methyl-branched fatty acid
Hydroxy acid
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Hydroxy fatty acids (LMFA01050393 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0000642)
Cell membrane (HMDB: HMDB0000642)

Organelle

Adiposome (HMDB: HMDB0000642)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0000642)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0000642)

Source

Endogenous

Endogenous (HMDB: HMDB0000642)

Animal

Animal (HMDB: HMDB0000642)

Exogenous

Food

Food (HMDB: HMDB0000642)

Animal origin

Poultry

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)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

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)

Equine

Horse (FooDB: FOOD00378)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0000642)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0000642)

Lipid metabolism pathway (HMDB: HMDB0000642)

Biochemical process

Lipid transport (HMDB: HMDB0000642)

Role

Biological role

Energy source (HMDB: HMDB0000642)

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	336 g/L	ALOGPS
logP	-0.13	ALOGPS
logP	0.16	ChemAxon
logS	0.45	ALOGPS
pKa (Strongest Acidic)	4.51	ChemAxon
pKa (Strongest Basic)	-2.8	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	2	ChemAxon
Refractivity	28.04 m³·mol⁻¹	ChemAxon
Polarizability	11.76 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
DeepCCS	[M+H]+	126.828	30932474
DeepCCS	[M-H]-	123.217	30932474
DeepCCS	[M-2H]-	160.489	30932474
DeepCCS	[M+Na]+	135.991	30932474
AllCCS	[M+H]+	129.9	32859911
AllCCS	[M+H-H2O]+	125.7	32859911
AllCCS	[M+NH4]+	133.7	32859911
AllCCS	[M+Na]+	134.9	32859911
AllCCS	[M-H]-	125.8	32859911
AllCCS	[M+Na-2H]-	129.2	32859911
AllCCS	[M+HCOO]-	132.8	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	2.0 minutes	32390414
Predicted by Siyang on May 30, 2022	9.2556 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.05 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	219.0 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	877.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	329.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	62.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	191.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	47.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	266.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	266.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	213.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	604.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	152.1 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	749.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	185.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	238.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	482.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	301.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	245.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Erythronilic acid	C[C@H](O)[C@@H](C)C(O)=O	2083.5	Standard polar	33892256
Erythronilic acid	C[C@H](O)[C@@H](C)C(O)=O	1019.9	Standard non polar	33892256
Erythronilic acid	C[C@H](O)[C@@H](C)C(O)=O	1040.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Erythronilic acid,1TMS,isomer #1	C[C@H](O[Si](C)(C)C)[C@@H](C)C(=O)O	1128.6	Semi standard non polar	33892256
Erythronilic acid,1TMS,isomer #2	C[C@H](O)[C@@H](C)C(=O)O[Si](C)(C)C	1061.3	Semi standard non polar	33892256
Erythronilic acid,2TMS,isomer #1	C[C@H](O[Si](C)(C)C)[C@@H](C)C(=O)O[Si](C)(C)C	1206.7	Semi standard non polar	33892256
Erythronilic acid,1TBDMS,isomer #1	C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](C)C(=O)O	1367.1	Semi standard non polar	33892256
Erythronilic acid,1TBDMS,isomer #2	C[C@H](O)[C@@H](C)C(=O)O[Si](C)(C)C(C)(C)C	1283.7	Semi standard non polar	33892256
Erythronilic acid,2TBDMS,isomer #1	C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](C)C(=O)O[Si](C)(C)C(C)(C)C	1646.1	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 - Erythronilic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Erythronilic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Erythronilic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Erythronilic acid GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Erythronilic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Erythronilic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Erythronilic 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 - Erythronilic acid 10V, Negative-QTOF	splash10-01b9-8900000000-6e362f577b3d827a8387	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Erythronilic acid 20V, Negative-QTOF	splash10-05fr-9100000000-6950ab2628a11bf6839a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Erythronilic acid 40V, Negative-QTOF	splash10-052f-9000000000-5278bf25a974c9f30369	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Erythronilic acid 10V, Positive-QTOF	splash10-0zgi-9400000000-aee3a280a6df1ae985b6	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Erythronilic acid 20V, Positive-QTOF	splash10-0002-9000000000-45e4e2c8c6ea7216859f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Erythronilic acid 40V, Positive-QTOF	splash10-052b-9000000000-845222220a578798d8ce	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

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

FDB022158

KNApSAcK ID

Not Available

Chemspider ID

9990501

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11815846

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Sugiyama, Yoshio; Miya, Hiroyuki; Kawada, Mitsuru. Process for producing optically active 3-hydroxy-2-methylbutyrates. PCT Int. Appl. (1991), 31 pp.

Material Safety Data Sheet (MSDS)

Not Available

General References

Heil M, Podebrad F, Prado E, Beck T, Mosand A, Sewell AC, Bohles H, Lehnert W: Enantioselective analysis of ketone bodies in patients with beta-ketothiolase deficiency, medium-chain acyl coenzyme A dehydrogenase deficiency and ketonemic vomiting. J Chromatogr B Biomed Sci Appl. 2000 Mar 10;739(2):313-24. [PubMed:10755375 ]

Showing metabocard for Erythronilic acid (HMDB0000642)

MOL for HMDB0000642 (Erythronilic acid)

3D MOL for HMDB0000642 (Erythronilic acid)

3D SDF for HMDB0000642 (Erythronilic acid)

3D-SDF for HMDB0000642 (Erythronilic acid)

PDB for HMDB0000642 (Erythronilic acid)

3D PDB for HMDB0000642 (Erythronilic acid)

SMILES for HMDB0000642 (Erythronilic acid)

INCHI for HMDB0000642 (Erythronilic acid)

Structure for HMDB0000642 (Erythronilic acid)

3D Structure for HMDB0000642 (Erythronilic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra