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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

2012-09-11 17:53:12 UTC

Update Date

2023-02-21 17:22:59 UTC

HMDB ID

HMDB0033007

Secondary Accession Numbers

HMDB33007

Metabolite Identification

Common Name

(2R,3R)-2,3-Butanediol

Description

(2R,3R)-2,3-Butanediol is found in cocoa and cocoa products. (2R,3R)-2,3-Butanediol is isolated from cocoa butter and roots of Ruta graveolens (rue).2,3-Butanediol is one of the constitutional isomers of butanediol. The 2R,3R stereoisomer of 2,3-butanediol is produced by a variety of microorganisms, in a process known as butanediol fermentation. It is found in cocoa butter and in the roots of Ruta graveolens. (Wikipedia).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(R,R)-(-)-Butane-2,3-diol	ChEBI
(R,R)-2,3-Butanediol	ChEBI
(R,R)-2,3-Butylene glycol	ChEBI
(-)-(2R,3R)-Butanediol	HMDB
(-)-2,3-Butanediol	HMDB
(2R,3R)-(-)-2,3-Butanediol	HMDB
(2R,3R)-Butane-2,3-diol	HMDB
L-(-)-2,3-Butanediol	HMDB
levo-2,3-Butanediol	HMDB

Chemical Formula

C₄H₁₀O₂

Average Molecular Weight

90.121

Monoisotopic Molecular Weight

90.068079564

IUPAC Name

(2R,3R)-butane-2,3-diol

Traditional Name

(R,R)-butane-2,3-diol

CAS Registry Number

24347-58-8

SMILES

C[C@@H](O)[C@@H](C)O

InChI Identifier

InChI=1S/C4H10O2/c1-3(5)4(2)6/h3-6H,1-2H3/t3-,4-/m1/s1

InChI Key

OWBTYPJTUOEWEK-QWWZWVQMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

1,2-diols

Alternative Parents

Substituents

Secondary alcohol
1,2-diol
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

butane-2,3-diol (CHEBI:16982 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0033007)
Cytoplasm (HMDB: HMDB0033007)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033007)

Source

Exogenous

Food

Food (HMDB: HMDB0033007)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Cocoa and cocoa products (FooDB: FOOD00860)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Plant

Plant (HMDB: HMDB0033007)
Theobroma cacao (HMDB: HMDB0033007)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033007)

Industrial application

Drug (HMDB: HMDB0033007)

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	19.7 °C	Not Available
Boiling Point	77.00 to 78.00 °C. @ 10.00 mm Hg	The Good Scents Company Information System
Water Solubility	759300 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	0.88	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	603 g/L	ALOGPS
logP	-0.59	ALOGPS
logP	-0.38	ChemAxon
logS	0.83	ALOGPS
pKa (Strongest Acidic)	14.22	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	23.39 m³·mol⁻¹	ChemAxon
Polarizability	9.82 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]+	117.954	31661259
DarkChem	[M-H]-	114.711	31661259
DeepCCS	[M+H]+	125.394	30932474
DeepCCS	[M-H]-	122.848	30932474
DeepCCS	[M-2H]-	158.877	30932474
DeepCCS	[M+Na]+	133.69	30932474
AllCCS	[M+H]+	126.3	32859911
AllCCS	[M+H-H2O]+	122.0	32859911
AllCCS	[M+NH4]+	130.4	32859911
AllCCS	[M+Na]+	131.6	32859911
AllCCS	[M-H]-	127.3	32859911
AllCCS	[M+Na-2H]-	132.0	32859911
AllCCS	[M+HCOO]-	137.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(2R,3R)-2,3-Butanediol	C[C@@H](O)[C@@H](C)O	1549.7	Standard polar	33892256
(2R,3R)-2,3-Butanediol	C[C@@H](O)[C@@H](C)O	760.1	Standard non polar	33892256
(2R,3R)-2,3-Butanediol	C[C@@H](O)[C@@H](C)O	753.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(2R,3R)-2,3-Butanediol,1TMS,isomer #1	C[C@@H](O)[C@@H](C)O[Si](C)(C)C	901.5	Semi standard non polar	33892256
(2R,3R)-2,3-Butanediol,2TMS,isomer #1	C[C@@H](O[Si](C)(C)C)[C@@H](C)O[Si](C)(C)C	1028.0	Semi standard non polar	33892256
(2R,3R)-2,3-Butanediol,1TBDMS,isomer #1	C[C@@H](O)[C@@H](C)O[Si](C)(C)C(C)(C)C	1123.9	Semi standard non polar	33892256
(2R,3R)-2,3-Butanediol,2TBDMS,isomer #1	C[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](C)O[Si](C)(C)C(C)(C)C	1483.2	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,3R)-2,3-Butanediol GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9000000000-cc27e53ef044f7cb15a5	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,3R)-2,3-Butanediol GC-MS (2 TMS) - 70eV, Positive	splash10-01b9-9520000000-fa7488838e20f2dd123b	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,3R)-2,3-Butanediol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2R,3R)-2,3-Butanediol 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,3R)-2,3-Butanediol 10V, Positive-QTOF	splash10-0006-9000000000-373d8ab05d8ca30b9936	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 20V, Positive-QTOF	splash10-006x-9000000000-c995422d63c292e20b8f	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 40V, Positive-QTOF	splash10-0a4i-9000000000-5639537d59074e5a4a6c	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 10V, Negative-QTOF	splash10-000i-9000000000-aa5e86f920a11ea2d749	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 20V, Negative-QTOF	splash10-000i-9000000000-cef0995334342db934ba	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 40V, Negative-QTOF	splash10-00di-9000000000-c4f65aef56394c6d3a25	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 10V, Positive-QTOF	splash10-0a4i-9000000000-2e058d12c0f9880bd53d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 20V, Positive-QTOF	splash10-0a4i-9000000000-77a30103f1d168eecd21	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 40V, Positive-QTOF	splash10-0002-9000000000-4c2f1d8ca7aa89a88c6c	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 10V, Negative-QTOF	splash10-000i-9000000000-09fc38b483234e7b66aa	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 20V, Negative-QTOF	splash10-000f-9000000000-79fde7f9417c0129ac4c	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (2R,3R)-2,3-Butanediol 40V, Negative-QTOF	splash10-0006-9000000000-452a5f79625d3401d495	2021-09-24	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

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

Cytoplasm
Extracellular

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

FDB010997

KNApSAcK ID

Not Available

Chemspider ID

196452

KEGG Compound ID

C03044

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

225936

PDB ID

Not Available

ChEBI ID

16982

Food Biomarker Ontology

Not Available

VMH ID

BTD_RR

MarkerDB ID

Not Available

Good Scents ID

rw1138431

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details

1. Ubiquitin-conjugating enzyme E2 D2

General function:: Involved in acid-amino acid ligase activity
Specific function:: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.
Gene Name:: UBE2D2
Uniprot ID:: P62837
Molecular weight:: 16735.06

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]

Showing metabocard for (2R,3R)-2,3-Butanediol (HMDB0033007)

MOL for HMDB0033007 ((2R,3R)-2,3-Butanediol)

3D MOL for HMDB0033007 ((2R,3R)-2,3-Butanediol)

3D SDF for HMDB0033007 ((2R,3R)-2,3-Butanediol)

3D-SDF for HMDB0033007 ((2R,3R)-2,3-Butanediol)

PDB for HMDB0033007 ((2R,3R)-2,3-Butanediol)

3D PDB for HMDB0033007 ((2R,3R)-2,3-Butanediol)

SMILES for HMDB0033007 ((2R,3R)-2,3-Butanediol)

INCHI for HMDB0033007 ((2R,3R)-2,3-Butanediol)

Structure for HMDB0033007 ((2R,3R)-2,3-Butanediol)

3D Structure for HMDB0033007 ((2R,3R)-2,3-Butanediol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

References