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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

Expected but not Quantified

Creation Date

2013-05-17 00:51:57 UTC

Update Date

2023-02-21 17:29:51 UTC

HMDB ID

HMDB0060309

Secondary Accession Numbers

HMDB60309

Metabolite Identification

Common Name

(2R)-2-Hydroxy-2-methylbutanenitrile

Description

(2R)-2-Hydroxy-2-methylbutanenitrile, also known as (2R)-2-hydroxy-2-cyanobutane or (R)-butan-2-one cyanohydrin, belongs to the class of organic compounds known as tertiary alcohols. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ) (2R)-2-Hydroxy-2-methylbutanenitrile is an extremely weak basic (essentially neutral) compound (based on its pKa) (2R)-2-Hydroxy-2-methylbutanenitrile exists in all living organisms, ranging from bacteria to humans. Outside of the human body, (2R)-2-Hydroxy-2-methylbutanenitrile has been detected, but not quantified in, several different foods, such as okra, beans, rocket salad, garden onions, and cabbages. This could make (2R)-2-hydroxy-2-methylbutanenitrile a potential biomarker for the consumption of these foods. These are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R â‰ H ).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(2R)-2-Hydroxy-2-cyanobutane	ChEBI
(2R)-2-Hydroxy-2-methylbutyronitrile	ChEBI
(R)-Butan-2-one cyanohydrin	ChEBI
2-Hydroxy-2-methylbutanenitrile	ChEBI

Chemical Formula

C₅H₉NO

Average Molecular Weight

99.1311

Monoisotopic Molecular Weight

99.068413915

IUPAC Name

(2R)-2-hydroxy-2-methylbutanenitrile

Traditional Name

(R)-butan-2-one cyanohydrin

CAS Registry Number

Not Available

SMILES

CC[C@@](C)(O)C#N

InChI Identifier

InChI=1S/C5H9NO/c1-3-5(2,7)4-6/h7H,3H2,1-2H3/t5-/m1/s1

InChI Key

VMEHOTODTPXCKT-RXMQYKEDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tertiary alcohols. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Tertiary alcohols

Alternative Parents

Substituents

Tertiary alcohol
Alpha-hydroxynitrile
Cyanohydrin
Nitrile
Carbonitrile
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2-hydroxy-2-methylbutanenitrile (CHEBI:60908 )

Ontology

Not Available

Exogenous (HMDB: HMDB0060309)

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	25.1 g/L	ALOGPS
logP	0.29	ALOGPS
logP	0.54	ChemAxon
logS	-0.6	ALOGPS
pKa (Strongest Acidic)	12.48	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	44.02 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	27.06 m³·mol⁻¹	ChemAxon
Polarizability	10.68 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]+	120.179	31661259
DarkChem	[M-H]-	118.368	31661259
DeepCCS	[M+H]+	124.461	30932474
DeepCCS	[M-H]-	122.385	30932474
DeepCCS	[M-2H]-	158.469	30932474
DeepCCS	[M+Na]+	133.191	30932474
AllCCS	[M+H]+	124.8	32859911
AllCCS	[M+H-H2O]+	120.4	32859911
AllCCS	[M+NH4]+	128.8	32859911
AllCCS	[M+Na]+	130.0	32859911
AllCCS	[M-H]-	125.4	32859911
AllCCS	[M+Na-2H]-	129.4	32859911
AllCCS	[M+HCOO]-	133.7	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.	1.58 minutes	32390414
Predicted by Siyang on May 30, 2022	11.4197 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.54 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1418.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	406.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	130.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	257.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	83.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	460.0 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	497.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	151.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	818.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	299.3 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	1077.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	282.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	301.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	495.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	422.7 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	103.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(2R)-2-Hydroxy-2-methylbutanenitrile	CC[C@@](C)(O)C#N	1367.8	Standard polar	33892256
(2R)-2-Hydroxy-2-methylbutanenitrile	CC[C@@](C)(O)C#N	805.9	Standard non polar	33892256
(2R)-2-Hydroxy-2-methylbutanenitrile	CC[C@@](C)(O)C#N	850.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(2R)-2-Hydroxy-2-methylbutanenitrile,1TMS,isomer #1	CC[C@](C)(C#N)O[Si](C)(C)C	970.1	Semi standard non polar	33892256
(2R)-2-Hydroxy-2-methylbutanenitrile,1TBDMS,isomer #1	CC[C@](C)(C#N)O[Si](C)(C)C(C)(C)C	1186.3	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 - (2R)-2-Hydroxy-2-methylbutanenitrile GC-MS (Non-derivatized) - 70eV, Positive	splash10-00fr-9000000000-88d46df9c2150f8b8f19	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile GC-MS (1 TMS) - 70eV, Positive	splash10-00g3-9400000000-97f3ec6e2fed4de1662f	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 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 - (2R)-2-Hydroxy-2-methylbutanenitrile 10V, Positive-QTOF	splash10-0ue9-8900000000-4b1cda9886763f383af9	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 20V, Positive-QTOF	splash10-0fsi-9200000000-6bfd1f380c40c2ad9643	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 40V, Positive-QTOF	splash10-014i-9000000000-43ffba1a5a84543676fe	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 10V, Negative-QTOF	splash10-0002-9000000000-e918a7872b51cd5fa521	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 20V, Negative-QTOF	splash10-0002-9000000000-2b3f108f5270636679b9	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 40V, Negative-QTOF	splash10-0g59-9000000000-1bdc857dd1d717408c15	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 10V, Positive-QTOF	splash10-001i-9000000000-159bda552f1b31948abe	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 20V, Positive-QTOF	splash10-0a59-9000000000-c14460958f25c8d2d4a9	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 40V, Positive-QTOF	splash10-0pb9-9000000000-8c9ec91e633b064112ed	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 10V, Negative-QTOF	splash10-001j-9000000000-3c520c286009b14fd6e6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 20V, Negative-QTOF	splash10-000t-9000000000-5fca23173994b620627f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R)-2-Hydroxy-2-methylbutanenitrile 40V, Negative-QTOF	splash10-0ue9-9000000000-1e04a2e96bbbdc1a5d46	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

FDB030109

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C18796

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12650900

PDB ID

Not Available

ChEBI ID

60908

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. Cytosolic beta-glucosidase

General function:: Involved in hydrolase activity, hydrolyzing O-glycosyl compounds
Specific function:: Glycosidase probably involved in the intestinal absorption and metabolism of dietary flavonoid glycosides. Able to hydrolyze a broad variety of glycosides including phytoestrogens, flavonols, flavones, flavanones and cyanogens. Possesses beta-glycosylceramidase activity and may be involved in a nonlysosomal catabolic pathway of glycosylceramide.
Gene Name:: GBA3
Uniprot ID:: Q9H227
Molecular weight:: Not Available

Reactions

Lotaustralin + Water → (2R)-2-Hydroxy-2-methylbutanenitrile + D-Glucose	details

Showing metabocard for (2R)-2-Hydroxy-2-methylbutanenitrile (HMDB0060309)

MOL for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

3D MOL for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

3D SDF for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

3D-SDF for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

PDB for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

3D PDB for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

SMILES for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

INCHI for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

Structure for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

3D Structure for HMDB0060309 ((2R)-2-Hydroxy-2-methylbutanenitrile)

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