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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 01:24:33 UTC

Update Date

2023-02-21 17:30:02 UTC

HMDB ID

HMDB0060490

Secondary Accession Numbers

HMDB60490

Metabolite Identification

Common Name

Methylselenopyruvate

Description

Methylselenopyruvate belongs to the class of organic compounds known as alpha-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the adjacent carbon. Methylselenopyruvate is an extremely weak basic (essentially neutral) compound (based on its pKa).

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-Methylselenopyruvate	Kegg
b-Methylselenopyruvate	Generator
b-Methylselenopyruvic acid	Generator
beta-Methylselenopyruvic acid	Generator
Β-methylselenopyruvate	Generator
Β-methylselenopyruvic acid	Generator
Methylselenopyruvic acid	Generator

Chemical Formula

C₄H₆O₃Se

Average Molecular Weight

181.05

Monoisotopic Molecular Weight

181.948215886

IUPAC Name

3-(methylselanyl)-2-oxopropanoic acid

Traditional Name

3-(methylselanyl)-2-oxopropanoic acid

CAS Registry Number

Not Available

SMILES

C[Se]CC(=O)C(O)=O

InChI Identifier

InChI=1S/C4H6O3Se/c1-8-2-3(5)4(6)7/h2H2,1H3,(H,6,7)

InChI Key

KCHPIRYOQIGZLW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the adjacent carbon.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Alpha-keto acids and derivatives

Direct Parent

Alpha-keto acids and derivatives

Alternative Parents

Substituents

Alpha-keto acid
Alpha-hydroxy ketone
Ketone
Selenoether
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organoselenium compound
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

oxo carboxylic acid (CHEBI:82049 )

Ontology

Not Available

Exogenous (HMDB: HMDB0060490)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

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	54.9 g/L	ALOGPS
logP	-0.47	ALOGPS
logP	0.33	ChemAxon
logS	-0.52	ALOGPS
pKa (Strongest Acidic)	2.16	ChemAxon
pKa (Strongest Basic)	-9.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	35.79 m³·mol⁻¹	ChemAxon
Polarizability	11.35 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]+	128.813	30932474
DeepCCS	[M-H]-	126.04	30932474
DeepCCS	[M-2H]-	162.626	30932474
DeepCCS	[M+Na]+	137.321	30932474
AllCCS	[M+H]+	135.5	32859911
AllCCS	[M+H-H2O]+	131.7	32859911
AllCCS	[M+NH4]+	139.1	32859911
AllCCS	[M+Na]+	140.1	32859911
AllCCS	[M-H]-	141.5	32859911
AllCCS	[M+Na-2H]-	144.7	32859911
AllCCS	[M+HCOO]-	148.3	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	881.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	321.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	78.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	212.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	56.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	245.5 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	263.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	591.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	588.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	74.4 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	779.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	203.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	236.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	611.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	297.8 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	285.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Methylselenopyruvate	C[Se]CC(=O)C(O)=O	1776.2	Standard polar	33892256
Methylselenopyruvate	C[Se]CC(=O)C(O)=O	1421.6	Standard non polar	33892256
Methylselenopyruvate	C[Se]CC(=O)C(O)=O	1602.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Methylselenopyruvate,1TMS,isomer #1	C[Se]CC(=O)C(=O)O[Si](C)(C)C	1307.3	Semi standard non polar	33892256
Methylselenopyruvate,1TMS,isomer #2	C[Se]C=C(O[Si](C)(C)C)C(=O)O	1428.4	Semi standard non polar	33892256
Methylselenopyruvate,2TMS,isomer #1	C[Se]C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1464.6	Semi standard non polar	33892256
Methylselenopyruvate,2TMS,isomer #1	C[Se]C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1277.8	Standard non polar	33892256
Methylselenopyruvate,2TMS,isomer #1	C[Se]C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1269.8	Standard polar	33892256
Methylselenopyruvate,1TBDMS,isomer #1	C[Se]CC(=O)C(=O)O[Si](C)(C)C(C)(C)C	1557.3	Semi standard non polar	33892256
Methylselenopyruvate,1TBDMS,isomer #2	C[Se]C=C(O[Si](C)(C)C(C)(C)C)C(=O)O	1662.9	Semi standard non polar	33892256
Methylselenopyruvate,2TBDMS,isomer #1	C[Se]C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1911.8	Semi standard non polar	33892256
Methylselenopyruvate,2TBDMS,isomer #1	C[Se]C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1682.2	Standard non polar	33892256
Methylselenopyruvate,2TBDMS,isomer #1	C[Se]C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1600.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Methylselenopyruvate GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9300000000-fa55d8e35020dfc887a4	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methylselenopyruvate GC-MS (1 TMS) - 70eV, Positive	splash10-00y0-9400000000-98006ffbe7b5b9a8b909	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methylselenopyruvate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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 - Methylselenopyruvate 10V, Positive-QTOF	splash10-001i-0900000000-fae31832f2765d747cfd	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 20V, Positive-QTOF	splash10-001i-1900000000-d110db3043cda5cbbad9	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 40V, Positive-QTOF	splash10-0006-7900000000-96ecb93529b1619adc72	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 10V, Negative-QTOF	splash10-01q9-3900000000-69f35542a7e43f206be7	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 20V, Negative-QTOF	splash10-001r-4900000000-9d8eb9021a2d7a73f649	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 40V, Negative-QTOF	splash10-0a4i-3900000000-11e14dce33b249382c68	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 10V, Positive-QTOF	splash10-03e9-0900000000-d55bb7006418fa7374f2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 20V, Positive-QTOF	splash10-052r-2900000000-72df6f77cd3868f8d98f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 40V, Positive-QTOF	splash10-0a4i-1900000000-84d6244c31320d88b12d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 10V, Negative-QTOF	splash10-001i-0900000000-46769265e5f64f4995e0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 20V, Negative-QTOF	splash10-0006-9000000000-a8e4ff3068cf37155804	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methylselenopyruvate 40V, Negative-QTOF	splash10-0006-9100000000-2110439293c25484af82	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
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, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX 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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C18904

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53297415

PDB ID

Not Available

ChEBI ID

82049

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

Enzyme Details

1. Kynurenine--oxoglutarate transaminase 1

General function:: Involved in 1-aminocyclopropane-1-carboxylate synthase activity
Specific function:: Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). Metabolizes the cysteine conjugates of certain halogenated alkenes and alkanes to form reactive metabolites. Catalyzes the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond.
Gene Name:: CCBL1
Uniprot ID:: Q16773
Molecular weight:: 47874.765

Reactions

Se-Methylselenocysteine + 2-Oxo-4-methylthiobutanoic acid → Methylselenopyruvate + Methionine	details

Enzyme Details

2. Kynurenine--oxoglutarate transaminase 3

General function:: Involved in transferase activity, transferring nitrogenous groups
Specific function:: Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). May catalyze the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond (By similarity). Has transaminase activity towards L-kynurenine, tryptophan, phenylalanine, serine, cysteine, methionine, histidine, glutamine and asparagine with glyoxylate as an amino group acceptor (in vitro). Has lower activity with 2-oxoglutarate as amino group acceptor (in vitro) (By similarity).
Gene Name:: CCBL2
Uniprot ID:: Q6YP21
Molecular weight:: 51399.855

Reactions

Se-Methylselenocysteine + 2-Oxo-4-methylthiobutanoic acid → Methylselenopyruvate + Methionine	details

Showing metabocard for Methylselenopyruvate (HMDB0060490)

MOL for HMDB0060490 (Methylselenopyruvate)

3D MOL for HMDB0060490 (Methylselenopyruvate)

3D SDF for HMDB0060490 (Methylselenopyruvate)

3D-SDF for HMDB0060490 (Methylselenopyruvate)

PDB for HMDB0060490 (Methylselenopyruvate)

3D PDB for HMDB0060490 (Methylselenopyruvate)

SMILES for HMDB0060490 (Methylselenopyruvate)

INCHI for HMDB0060490 (Methylselenopyruvate)

Structure for HMDB0060490 (Methylselenopyruvate)

3D Structure for HMDB0060490 (Methylselenopyruvate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions

Reactions