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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2023-02-21 17:14:51 UTC

HMDB ID

HMDB0000459

Secondary Accession Numbers

HMDB00459

Metabolite Identification

Common Name

3-Methylcrotonylglycine

Description

3-Methylcrotonylglycine is an acyl glycine. Acyl glycines are normally minor metabolites of fatty acids. However, the excretion of certain acyl glycines is increased in several inborn errors of metabolism. In certain cases the measurement of these metabolites in body fluids can be used to diagnose disorders associated with mitochondrial fatty acid beta-oxidation. Acyl glycines are produced through the action of glycine N-acyltransferase (EC 2.3.1.13) which is an enzyme that catalyzes the chemical reaction: acyl-CoA + glycine < -- > CoA + N-acylglycine. 3-Methylcrotonylglycine is a normal amino acid metabolite found in urine. Increased levels of this metabolite are found in patients suffering from leucine catabolic disorders, such as 3-methylcrotonyl-CoA carboxylase deficiency. 3-Methylcrotonylglycine is often considered to be a diagnostic marker of organic acidemias (PMID 11170888 ). Moreover, 3-methylcrotonylglycine is found to be associated with 3-hydroxy-3-methylglutaryl-CoA lyase deficiency and propionic acidemia, which are also inborn errors of metabolism.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
beta-Methylcrotonylglycine	ChEBI
b-Methylcrotonylglycine	Generator
Β-methylcrotonylglycine	Generator
3-Methylcrotonyl glycine	HMDB
3-Methylcrotonyl-glycine	HMDB
3-Methylcrotonylglycin	HMDB
N-(3-Methyl-1-oxo-2-butenyl)-glycine	HMDB
3-Methylcrotonylglycine	MeSH

Chemical Formula

C₇H₁₁NO₃

Average Molecular Weight

157.1671

Monoisotopic Molecular Weight

157.073893223

IUPAC Name

2-(3-methylbut-2-enamido)acetic acid

Traditional Name

(3-methylbut-2-enamido)acetic acid

CAS Registry Number

33008-07-0

SMILES

CC(C)=CC(=O)NCC(O)=O

InChI Identifier

InChI=1S/C7H11NO3/c1-5(2)3-6(9)8-4-7(10)11/h3H,4H2,1-2H3,(H,8,9)(H,10,11)

InChI Key

PFWQSHXPNKRLIV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-alpha amino acids. N-acyl-alpha amino acids are compounds containing an alpha amino acid which bears an acyl group at its terminal nitrogen atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-acyl-alpha amino acids

Alternative Parents

Substituents

N-acyl-alpha-amino acid
N-acyl-amine
Secondary carboxylic acid amide
Carboxamide group
Monocarboxylic acid or derivatives
Carboxylic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

N-acylglycine (CHEBI:68499 )

Ontology

Not Available

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	7.64 g/L	ALOGPS
logP	0.02	ALOGPS
logP	0.058	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	4.09	ChemAxon
pKa (Strongest Basic)	-0.54	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.4 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	40.05 m³·mol⁻¹	ChemAxon
Polarizability	15.79 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]+	134.328	31661259
DarkChem	[M-H]-	130.466	31661259
AllCCS	[M+H]+	135.47	32859911
AllCCS	[M-H]-	133.777	32859911
DeepCCS	[M+H]+	131.337	30932474
DeepCCS	[M-H]-	127.509	30932474
DeepCCS	[M-2H]-	164.664	30932474
DeepCCS	[M+Na]+	140.104	30932474
AllCCS	[M+H]+	135.5	32859911
AllCCS	[M+H-H2O]+	131.5	32859911
AllCCS	[M+NH4]+	139.1	32859911
AllCCS	[M+Na]+	140.2	32859911
AllCCS	[M-H]-	133.8	32859911
AllCCS	[M+Na-2H]-	135.8	32859911
AllCCS	[M+HCOO]-	138.0	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.	2.59 minutes	32390414
Predicted by Siyang on May 30, 2022	10.0309 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.93 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	58.2 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1261.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	307.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	92.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	177.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	54.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	277.9 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	368.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	77.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	696.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	290.6 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	991.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	215.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	262.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	445.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	257.3 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	94.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Methylcrotonylglycine	CC(C)=CC(=O)NCC(O)=O	2274.0	Standard polar	33892256
3-Methylcrotonylglycine	CC(C)=CC(=O)NCC(O)=O	1277.8	Standard non polar	33892256
3-Methylcrotonylglycine	CC(C)=CC(=O)NCC(O)=O	1554.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Methylcrotonylglycine,1TMS,isomer #1	CC(C)=CC(=O)NCC(=O)O[Si](C)(C)C	1566.6	Semi standard non polar	33892256
3-Methylcrotonylglycine,1TMS,isomer #2	CC(C)=CC(=O)N(CC(=O)O)[Si](C)(C)C	1581.1	Semi standard non polar	33892256
3-Methylcrotonylglycine,2TMS,isomer #1	CC(C)=CC(=O)N(CC(=O)O[Si](C)(C)C)[Si](C)(C)C	1582.0	Semi standard non polar	33892256
3-Methylcrotonylglycine,2TMS,isomer #1	CC(C)=CC(=O)N(CC(=O)O[Si](C)(C)C)[Si](C)(C)C	1588.8	Standard non polar	33892256
3-Methylcrotonylglycine,2TMS,isomer #1	CC(C)=CC(=O)N(CC(=O)O[Si](C)(C)C)[Si](C)(C)C	1734.7	Standard polar	33892256
3-Methylcrotonylglycine,1TBDMS,isomer #1	CC(C)=CC(=O)NCC(=O)O[Si](C)(C)C(C)(C)C	1790.6	Semi standard non polar	33892256
3-Methylcrotonylglycine,1TBDMS,isomer #2	CC(C)=CC(=O)N(CC(=O)O)[Si](C)(C)C(C)(C)C	1793.0	Semi standard non polar	33892256
3-Methylcrotonylglycine,2TBDMS,isomer #1	CC(C)=CC(=O)N(CC(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2023.2	Semi standard non polar	33892256
3-Methylcrotonylglycine,2TBDMS,isomer #1	CC(C)=CC(=O)N(CC(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2020.4	Standard non polar	33892256
3-Methylcrotonylglycine,2TBDMS,isomer #1	CC(C)=CC(=O)N(CC(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2010.2	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Fibroblasts

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Detected and Quantified	<10 umol/mmol creatinine	Children (1 - 18 years old)	Both	Normal	BC Children's Hos...	details
Urine	Detected and Quantified	0.9-2.0 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	27012787	details
Urine	Detected and Quantified	0.8-1.2 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	27012787	details
Urine	Detected and Quantified	0.0559–0.6455 umol/mmol creatinine	Adult (25-30 years old)	Both	Not Available	23062437	details
Urine	Detected and Quantified	0.040.0–0.6236 umol/mmol creatinine	Adult (25-30 years old)	Both	Not Available	23062437	details
Urine	Detected and Quantified	0.0651–0.4442 umol/mmol creatinine	Adult (25-30 years old)	Both	Not Available	23062437	details
Urine	Detected but not Quantified	Not Quantified	Adult (24-38years old)	Not Specified	Normal	20971021	details
Urine	Detected and Quantified	<0.48 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	28853722	details
Urine	Detected and Quantified	6.100 +/- 4.100 umol/mmol creatinine	Not Specified	Not Specified	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	<2 umol/mmol creatinine	Not Specified	Not Specified	Normal	23705938	details
Urine	Detected and Quantified	0-2 umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	31506554	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected and Quantified	225.0 (0.00-450.0) umol/mmol creatinine	Children (1-13 years old)	Both	3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency	MetaGene: Metabol...	details
Urine	Detected and Quantified	700.0 (400.0-1000.0) umol/mmol creatinine	Children (1-13 years old)	Both	3-Methyl-Crotonyl-Glycinuria	MetaGene: Metabol...	details
Urine	Detected and Quantified	27.5 (5.0-50.0) umol/mmol creatinine	Children (1-13 years old)	Both	Biotinidase deficiency	MetaGene: Metabol...	details
Urine	Detected and Quantified	0.41 umol/mmol creatinine	Adult (>18 years old)	Not Specified	Propionic acidemia	28853722	details
Urine	Detected and Quantified	27.6 umol/mmol creatinine	Newborn (0-30 days old)	Male	3-hydroxy-3-methylglutaric- coenzyme A lyase deficiency	23705938	details
Urine	Detected and Quantified	120 umol/mmol creatinine	Children (1 - 13 years old)	Female	3-Methylcrotonyl-CoA Carboxylase Deficiency	7474896	details
Urine	Detected and Quantified	1975 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Isolated 3-Methylcrotonyl-CoA Carboxylase Deficiency	11893004	details
Urine	Detected and Quantified	27.6 umol/mmol creatinine	Newborn (0-30 days old)	Male	3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency	23705938	details

Associated Disorders and Diseases

Disease References

3-Hydroxy-3-methylglutaryl-CoA lyase deficiency
Santarelli F, Cassanello M, Enea A, Poma F, D'Onofrio V, Guala G, Garrone G, Puccinelli P, Caruso U, Porta F, Spada M: A neonatal case of 3-hydroxy-3-methylglutaric-coenzyme A lyase deficiency. Ital J Pediatr. 2013 May 24;39:33. doi: 10.1186/1824-7288-39-33. [PubMed:23705938 ] G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
3-Methyl-crotonyl-glycinuria
Rutledge SL, Berry GT, Stanley CA, van Hove JL, Millington D: Glycine and L-carnitine therapy in 3-methylcrotonyl-CoA carboxylase deficiency. J Inherit Metab Dis. 1995;18(3):299-305. [PubMed:7474896 ] de Kremer RD, Latini A, Suormala T, Baumgartner ER, Larovere L, Civallero G, Guelbert N, Paschini-Capra A, Depetris-Boldini C, Mayor CQ: Leukodystrophy and CSF purine abnormalities associated with isolated 3-methylcrotonyl-CoA carboxylase deficiency. Metab Brain Dis. 2002 Mar;17(1):13-8. [PubMed:11893004 ] G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Biotinidase deficiency
G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Propionic acidemia
Riemersma M, Hazebroek MR, Helderman-van den Enden ATJM, Salomons GS, Ferdinandusse S, Brouwers MCGJ, van der Ploeg L, Heymans S, Glatz JFC, van den Wijngaard A, Krapels IPC, Bierau J, Brunner HG: Propionic acidemia as a cause of adult-onset dilated cardiomyopathy. Eur J Hum Genet. 2017 Nov;25(11):1195-1201. doi: 10.1038/ejhg.2017.127. Epub 2017 Aug 30. [PubMed:28853722 ]

Associated OMIM IDs

246450 (3-Hydroxy-3-methylglutaryl-CoA lyase deficiency)
210200 (3-Methyl-crotonyl-glycinuria)
253260 (Biotinidase deficiency)
606054 (Propionic acidemia)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022057

KNApSAcK ID

Not Available

Chemspider ID

148224

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5447

PubChem Compound

169485

PDB ID

Not Available

ChEBI ID

68499

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

MDB00013425

Good Scents ID

Not Available

References

Synthesis Reference

Carter, S. M. Bonham; Watson, D. G.; Midgley, J. M.; Logan, R. W. Synthesis and characterization of acyl glycines. Their measurement in single blood spots by gas chromatography-mass spectrometry to diagnose inborn errors of metabolism. Journal of Chromatography, B: Biomedical Applications (1996), 677(1), 29-35.

Material Safety Data Sheet (MSDS)

Not Available

General References

Gallardo ME, Desviat LR, Rodriguez JM, Esparza-Gordillo J, Perez-Cerda C, Perez B, Rodriguez-Pombo P, Criado O, Sanz R, Morton DH, Gibson KM, Le TP, Ribes A, de Cordoba SR, Ugarte M, Penalva MA: The molecular basis of 3-methylcrotonylglycinuria, a disorder of leucine catabolism. Am J Hum Genet. 2001 Feb;68(2):334-46. Epub 2001 Jan 17. [PubMed:11170888 ]
Chantin C, Bonin B, Boulieu R, Bory C: Liquid-chromatographic study of purine metabolism abnormalities in purine nucleoside phosphorylase deficiency. Clin Chem. 1996 Feb;42(2):326-8. [PubMed:8595732 ]
Wysocki SJ, Hahnel R: 3-Methylcrotonylglycine excretion in 3-hydroxy-3-methylglutaric aciduria. Clin Chim Acta. 1978 May 16;86(1):101-8. [PubMed:657530 ]
Koeberl DD, Millington DS, Smith WE, Weavil SD, Muenzer J, McCandless SE, Kishnani PS, McDonald MT, Chaing S, Boney A, Moore E, Frazier DM: Evaluation of 3-methylcrotonyl-CoA carboxylase deficiency detected by tandem mass spectrometry newborn screening. J Inherit Metab Dis. 2003;26(1):25-35. [PubMed:12872837 ]
Baykal T, Gokcay GH, Ince Z, Dantas MF, Fowler B, Baumgartner MR, Demir F, Can G, Demirkol M: Consanguineous 3-methylcrotonyl-CoA carboxylase deficiency: early-onset necrotizing encephalopathy with lethal outcome. J Inherit Metab Dis. 2005;28(2):229-33. [PubMed:15877210 ]
Cowan MJ, Wara DW, Packman S, Ammann AJ, Yoshino M, Sweetman L, Nyhan W: Multiple biotin-dependent carboxylase deficiencies associated with defects in T-cell and B-cell immunity. Lancet. 1979 Jul 21;2(8134):115-8. [PubMed:88554 ]

Enzymes

Enzyme Details

1. Glycine N-acyltransferase

General function:: Involved in glycine N-acyltransferase activity
Specific function:: Mitochondrial acyltransferase which transfers an acyl group to the N-terminus of glycine and glutamine, although much less efficiently. Can conjugate numerous substrates to form a variety of N-acylglycines, with a preference for benzoyl-CoA over phenylacetyl-CoA as acyl donors. Thereby detoxify xenobiotics, such as benzoic acid or salicylic acid, and endogenous organic acids, such as isovaleric acid.
Gene Name:: GLYAT
Uniprot ID:: Q6IB77
Molecular weight:: 18506.33

Enzyme Details

2. Glycine N-acyltransferase-like protein 1

General function:: Involved in glycine N-acyltransferase activity
Specific function:: Acyltransferase which transfers an acyl group to the N-terminus of glutamine. Can use phenylacetyl-CoA as an acyl donor.
Gene Name:: GLYATL1
Uniprot ID:: Q969I3
Molecular weight:: 35100.895

Enzyme Details

3. Glycine N-acyltransferase-like protein 2

General function:: Involved in glycine N-acyltransferase activity
Specific function:: Mitochondrial acyltransferase which transfers the acyl group to the N-terminus of glycine. Conjugates numerous substrates, such as arachidonoyl-CoA and saturated medium and long-chain acyl-CoAs ranging from chain-length C8:0-CoA to C18:0-CoA, to form a variety of N-acylglycines. Shows a preference for monounsaturated fatty acid oleoyl-CoA (C18:1-CoA) as an acyl donor. Does not exhibit any activity toward C22:6-CoA and chenodeoxycholoyl-CoA, nor toward serine or alanine.
Gene Name:: GLYATL2
Uniprot ID:: Q8WU03
Molecular weight:: 34277.055

Enzyme Details

4. Glycine N-acyltransferase-like protein 3

General function:: Involved in glycine N-acyltransferase activity
Specific function:: Acyltransferase which transfers the acyl group to the N- terminus of glycine
Gene Name:: GLYATL3
Uniprot ID:: Q5SZD4
Molecular weight:: 32703.3

Showing metabocard for 3-Methylcrotonylglycine (HMDB0000459)

MOL for HMDB0000459 (3-Methylcrotonylglycine)

3D MOL for HMDB0000459 (3-Methylcrotonylglycine)

3D SDF for HMDB0000459 (3-Methylcrotonylglycine)

3D-SDF for HMDB0000459 (3-Methylcrotonylglycine)

PDB for HMDB0000459 (3-Methylcrotonylglycine)

3D PDB for HMDB0000459 (3-Methylcrotonylglycine)

SMILES for HMDB0000459 (3-Methylcrotonylglycine)

INCHI for HMDB0000459 (3-Methylcrotonylglycine)

Structure for HMDB0000459 (3-Methylcrotonylglycine)

3D Structure for HMDB0000459 (3-Methylcrotonylglycine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes