Human Metabolome Database: Showing metabocard for 3-Methylcrotonylglycine (HMDB0000459)

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

enzymes (4) Show 4 proteins

Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2018-05-20 20:23:03 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 SDF 3D-SDF PDB SMILES InChI View 3D Structure

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

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

This compound belongs to the class of organic compounds known as n-acyl-alpha amino acids. These 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

Disposition

Source:

Endogenous

Biological location:

Cell and elements:

Cell:

Fibroblast

Subcellular:

Cytoplasm

Biofluid and excreta:

Role

Biological role:

Metabolite

Physical Properties

State

Solid

Experimental 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

Predicted 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)	1.01	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	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001l-9200000000-b5de5c506d0864c0f7d1	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-01x3-9210000000-3cd3c3c8ea08c7d1e6c7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-001i-9000000000-de6b64abad08a6b0aa93	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0a59-9000000000-6614867cbb98a3422626	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0a59-9000000000-87fe2c98c5568e0a3651	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-7900000000-f113c2d59fe1238ea573	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a6r-9100000000-ca7eb3d4b533d2e31892	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-78c1b06293f14b96b012	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0900000000-9462ca1f1e0bcf30b871	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-6900000000-7cf2a248f3b7490e7677	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ab9-9000000000-30da48e2c1ce30e69097	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Fibroblasts

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified		Not Available	Not Available	Normal		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		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	0.9-2.0 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	27012787	details
Urine	Detected and Quantified	<2 umol/mmol creatinine	Not Specified	Not Specified	Normal	23705938	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	6.100 +/- 4.100 umol/mmol creatinine	Not Specified	Not Specified	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	0.8-1.2 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	27012787	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	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
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

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

FoodDB 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

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)

Structure for HMDB0000459 (3-Methylcrotonylglycine)

Enzymes