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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2020-06-03 16:21:17 UTC

Update Date

2022-09-22 18:34:32 UTC

HMDB ID

HMDB0240650

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Ectoine

Description

ectoine belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. ectoine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on ectoine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(+)-1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid	ChEBI
L-Ectoine	ChEBI
(4S)-2-Methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate	Kegg
(+)-1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylate	Generator
(4S)-2-Methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid	Generator
1,4,5,6-tetrahydro-2-Methyl-4-pyrimidinecarboxylic acid	MeSH, HMDB
Ectoin	MeSH, HMDB
(4S)-2-Methyl-3,4,5,6-tetrahydropyrimidine-4-carboxylic acid	HMDB
(4S)-3,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid	HMDB
(S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid	HMDB
Ectoine	HMDB
Pyrostatin B	HMDB
Pyrostatine B	HMDB

Chemical Formula

C₆H₁₀N₂O₂

Average Molecular Weight

142.1558

Monoisotopic Molecular Weight

142.074227574

IUPAC Name

(4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid

Traditional Name

ectoine

CAS Registry Number

96702-03-3

SMILES

CC1=NCC[C@H](N1)C(O)=O

InChI Identifier

InChI=1S/C6H10N2O2/c1-4-7-3-2-5(8-4)6(9)10/h5H,2-3H2,1H3,(H,7,8)(H,9,10)/t5-/m0/s1

InChI Key

WQXNXVUDBPYKBA-YFKPBYRVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Hydropyrimidine carboxylic acid derivative
Hydropyrimidine
1,4,5,6-tetrahydropyrimidine
Imidolactam
Amidine
Carboxylic acid amidine
Carboxylic acid
Monocarboxylic acid or derivatives
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Azacycle
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Organic oxide
Organopnictogen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

monocarboxylic acid (CHEBI:27592 )
carboxamidine (CHEBI:27592 )
1,4,5,6-tetrahydropyrimidines (CHEBI:27592 )

Ontology

Not Available

Urine (PMID: 22409530)

Source

Exogenous

Exogenous (HMDB: HMDB0240650)

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
logP	-0.23	ALOGPS
logP	-2.5	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	2.75	ChemAxon
pKa (Strongest Basic)	10.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	61.69 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	35.04 m³·mol⁻¹	ChemAxon
Polarizability	14.25 Å³	ChemAxon
Number of Rings	1	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]+	128.307	30932474
DeepCCS	[M-H]-	124.467	30932474
DeepCCS	[M-2H]-	161.996	30932474
DeepCCS	[M+Na]+	137.375	30932474
AllCCS	[M+H]+	130.5	32859911
AllCCS	[M+H-H2O]+	125.9	32859911
AllCCS	[M+NH4]+	134.7	32859911
AllCCS	[M+Na]+	135.9	32859911
AllCCS	[M-H]-	127.2	32859911
AllCCS	[M+Na-2H]-	128.9	32859911
AllCCS	[M+HCOO]-	130.9	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.	0.4 minutes	32390414
Predicted by Siyang on May 30, 2022	8.8317 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	6.77 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	549.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	288.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	70.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	170.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	51.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	252.7 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	236.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	536.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	577.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	101.1 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	766.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	180.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	170.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	542.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	292.2 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	191.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Ectoine	CC1=NCC[C@H](N1)C(O)=O	2333.5	Standard polar	33892256
Ectoine	CC1=NCC[C@H](N1)C(O)=O	1233.3	Standard non polar	33892256
Ectoine	CC1=NCC[C@H](N1)C(O)=O	1515.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Ectoine,1TMS,isomer #1	CC1=NCC[C@@H](C(=O)O[Si](C)(C)C)N1	1412.8	Semi standard non polar	33892256
Ectoine,1TMS,isomer #2	CC1=NCC[C@@H](C(=O)O)N1[Si](C)(C)C	1564.7	Semi standard non polar	33892256
Ectoine,2TMS,isomer #1	CC1=NCC[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	1543.1	Semi standard non polar	33892256
Ectoine,2TMS,isomer #1	CC1=NCC[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	1463.5	Standard non polar	33892256
Ectoine,2TMS,isomer #1	CC1=NCC[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	2192.9	Standard polar	33892256
Ectoine,1TBDMS,isomer #1	CC1=NCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1	1652.3	Semi standard non polar	33892256
Ectoine,1TBDMS,isomer #2	CC1=NCC[C@@H](C(=O)O)N1[Si](C)(C)C(C)(C)C	1776.0	Semi standard non polar	33892256
Ectoine,2TBDMS,isomer #1	CC1=NCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	1945.8	Semi standard non polar	33892256
Ectoine,2TBDMS,isomer #1	CC1=NCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	1945.4	Standard non polar	33892256
Ectoine,2TBDMS,isomer #1	CC1=NCC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	2297.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Ectoine 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ectoine 50V, Positive-QTOF	splash10-0007-5900000000-f2bf01bf09de376591c4	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ectoine 50V, Negative-QTOF	splash10-0006-0900000000-0df36d79991c1fa4a82c	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ectoine 10V, Positive-QTOF	splash10-0006-2900000000-461b411f6b09403b5694	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ectoine 20V, Positive-QTOF	splash10-0002-9100000000-07a8428071aadde90d22	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ectoine 40V, Positive-QTOF	splash10-0aba-9000000000-e10d9e3345119cd297cb	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ectoine 10V, Negative-QTOF	splash10-0006-0900000000-45064a2e85c935d3a95b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ectoine 20V, Negative-QTOF	splash10-0006-8900000000-6dd41398500425af5df0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ectoine 40V, Negative-QTOF	splash10-0006-9000000000-fc9f75ff6724724b27cd	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	22409530	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Ectoine

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

27592

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1731791

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Zhang T, Creek DJ, Barrett MP, Blackburn G, Watson DG: Evaluation of coupling reversed phase, aqueous normal phase, and hydrophilic interaction liquid chromatography with Orbitrap mass spectrometry for metabolomic studies of human urine. Anal Chem. 2012 Feb 21;84(4):1994-2001. doi: 10.1021/ac2030738. Epub 2012 Feb 1. [PubMed:22409530 ]
Mair RD, Sirich TL, Plummer NS, Meyer TW: Characteristics of Colon-Derived Uremic Solutes. Clin J Am Soc Nephrol. 2018 Sep 7;13(9):1398-1404. doi: 10.2215/CJN.03150318. Epub 2018 Aug 7. [PubMed:30087103 ]

Enzymes

Enzyme Details

1. L-ectoine synthase

General function:: Not Available
Specific function:: Catalyzes the circularization of gamma-N-acetyl-alpha,gamma-diaminobutyric acid (ADABA) to ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid), which is an excellent osmoprotectant.
Gene Name:: ECTC
Uniprot ID:: B4R981
Molecular weight:: 14628.525

Showing metabocard for Ectoine (HMDB0240650)

MOL for HMDB0240650 (Ectoine)

3D MOL for HMDB0240650 (Ectoine)

3D SDF for HMDB0240650 (Ectoine)

3D-SDF for HMDB0240650 (Ectoine)

PDB for HMDB0240650 (Ectoine)

3D PDB for HMDB0240650 (Ectoine)

SMILES for HMDB0240650 (Ectoine)

INCHI for HMDB0240650 (Ectoine)

Structure for HMDB0240650 (Ectoine)

3D Structure for HMDB0240650 (Ectoine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes