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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (3) Show 3 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:33:12 UTC

Update Date

2023-02-21 17:19:21 UTC

HMDB ID

HMDB0029878

Secondary Accession Numbers

HMDB29878

Metabolite Identification

Common Name

D-Tartaric acid

Description

D-Tartaric acid, also known as (S,S)-tartrate or D-threaric acid, belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. D-Tartaric acid has been detected, but not quantified in, loquats (Eriobotrya japonica). This could make D-tartaric acid a potential biomarker for the consumption of these foods. D-Tartaric acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on D-Tartaric acid.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(-)-(S,S)-Tartaric acid	ChEBI
(-)-D-Tartaric acid	ChEBI
(-)-Tartaric acid	ChEBI
(-)-Weinsaeure	ChEBI
(2S,3S)-(-)-Tartaric acid	ChEBI
(2S,3S)-Tartaric acid	ChEBI
(S,S)-(-)-Tartaric acid	ChEBI
(S,S)-Tartaric acid	ChEBI
D(-)-TARTARIC ACID	ChEBI
D-(-)-Tartaric acid	ChEBI
D-Threaric acid	ChEBI
Linksweinsaeure	ChEBI
(S,S)-Tartrate	Kegg
D-Tartrate	Kegg
(-)-(S,S)-Tartarate	Generator
(-)-D-Tartarate	Generator
(-)-Tartarate	Generator
(2S,3S)-(-)-Tartarate	Generator
(2S,3S)-Tartarate	Generator
(S,S)-(-)-Tartarate	Generator
(S,S)-Tartarate	Generator
D(-)-TARTARate	Generator
D-(-)-Tartarate	Generator
D-Threarate	Generator
(S,S)-Tartric acid	Generator
D-Tartric acid	Generator
D-Tartarate	Generator
(2S,3S)-2,3-Dihydroxybutanedioic acid	HMDB
Tartrate	HMDB
Calcium tartrate	MeSH
Tartaric acid, ((r,r)-(+-))-isomer	MeSH
(R,r)-(+-)-2,3-dihydroxybutanedioic acid, monoammonium monosodium salt	MeSH
Aluminum tartrate	MeSH
Sodium ammonium tartrate	MeSH
Tartaric acid, (R-(r,r))-isomer	MeSH
Tartaric acid, (S-(r,r))-isomer	MeSH
Ammonium tartrate	MeSH
Calcium tartrate tetrahydrate	MeSH
Potassium tartrate	MeSH
Seignette salt	MeSH
Sodium potassium tartrate	MeSH
Stannous tartrate	MeSH
Tartaric acid	MeSH
Tartaric acid, (r,s)-isomer	MeSH
Tartaric acid, ammonium sodium salt, (1:1:1) salt, (r,r)-(+-)-isomer	MeSH
Tartaric acid, calcium salt, (R-r,r)-isomer	MeSH
MN(III) tartrate	MeSH
Sodium tartrate	MeSH
Tartaric acid, monoammonium salt, (R-(r,r))-isomer	MeSH

Chemical Formula

C₄H₆O₆

Average Molecular Weight

150.0868

Monoisotopic Molecular Weight

150.016437924

IUPAC Name

(2S,3S)-2,3-dihydroxybutanedioic acid

Traditional Name

D-tartaric acid

CAS Registry Number

147-71-7

SMILES

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

InChI Identifier

InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m0/s1

InChI Key

FEWJPZIEWOKRBE-LWMBPPNESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Short-chain hydroxy acid
Sugar acid
Monosaccharide
Hydroxy acid
Dicarboxylic acid or derivatives
Alpha-hydroxy acid
Fatty acid
Secondary alcohol
1,2-diol
Carboxylic acid
Carboxylic acid derivative
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

tartaric acid (CHEBI:15672 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0029878)
Cytoplasm (HMDB: HMDB0029878)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029878)

Source

Exogenous

Exogenous (HMDB: HMDB0029878)

Food

Food (HMDB: HMDB0029878)

Fruit

Tropical fruit

Loquat (FooDB: FOOD00076)

Endogenous

Endogenous (HMDB: HMDB0029878)

Plant

Plant (HMDB: HMDB0029878)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	169 - 170 °C	Not Available
Boiling Point	399.26 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	1000000 mg/L @ 25 °C (exp)	The Good Scents Company Information System
LogP	-1.081 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Not Available	117.95	http://allccs.zhulab.cn/database/detail?ID=AllCCS00002180

Predicted Molecular Properties

Property	Value	Source
Water Solubility	161 g/L	ALOGPS
logP	-1.3	ALOGPS
logP	-1.8	ChemAxon
logS	0.03	ALOGPS
pKa (Strongest Acidic)	2.72	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115.06 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	26.21 m³·mol⁻¹	ChemAxon
Polarizability	11.61 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]+	130.328	31661259
DarkChem	[M-H]-	126.776	31661259
DeepCCS	[M+H]+	126.226	30932474
DeepCCS	[M-H]-	123.608	30932474
DeepCCS	[M-2H]-	159.485	30932474
DeepCCS	[M+Na]+	134.783	30932474
AllCCS	[M+H]+	134.9	32859911
AllCCS	[M+H-H2O]+	130.9	32859911
AllCCS	[M+NH4]+	138.6	32859911
AllCCS	[M+Na]+	139.7	32859911
AllCCS	[M-H]-	122.5	32859911
AllCCS	[M+Na-2H]-	124.6	32859911
AllCCS	[M+HCOO]-	127.0	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.	0.89 minutes	32390414
Predicted by Siyang on May 30, 2022	10.5396 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	6.26 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	342.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	714.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	403.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	37.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	253.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	124.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	311.1 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	258.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	762.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	661.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	54.8 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	858.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	248.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	351.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	800.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	357.3 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	478.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
D-Tartaric acid	O[C@@H]([C@H](O)C(O)=O)C(O)=O	2468.8	Standard polar	33892256
D-Tartaric acid	O[C@@H]([C@H](O)C(O)=O)C(O)=O	1229.6	Standard non polar	33892256
D-Tartaric acid	O[C@@H]([C@H](O)C(O)=O)C(O)=O	1414.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Tartaric acid,1TMS,isomer #1	C[Si](C)(C)O[C@H](C(=O)O)[C@H](O)C(=O)O	1393.8	Semi standard non polar	33892256
D-Tartaric acid,1TMS,isomer #2	C[Si](C)(C)OC(=O)[C@@H](O)[C@H](O)C(=O)O	1372.7	Semi standard non polar	33892256
D-Tartaric acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H](O[Si](C)(C)C)[C@H](O)C(=O)O	1459.4	Semi standard non polar	33892256
D-Tartaric acid,2TMS,isomer #2	C[Si](C)(C)O[C@H](C(=O)O)[C@H](O[Si](C)(C)C)C(=O)O	1490.2	Semi standard non polar	33892256
D-Tartaric acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)[C@@H](O)[C@H](O[Si](C)(C)C)C(=O)O	1471.2	Semi standard non polar	33892256
D-Tartaric acid,2TMS,isomer #4	C[Si](C)(C)OC(=O)[C@@H](O)[C@H](O)C(=O)O[Si](C)(C)C	1461.5	Semi standard non polar	33892256
D-Tartaric acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)C(=O)O	1549.0	Semi standard non polar	33892256
D-Tartaric acid,3TMS,isomer #2	C[Si](C)(C)OC(=O)[C@@H](O)[C@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1567.0	Semi standard non polar	33892256
D-Tartaric acid,4TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1665.8	Semi standard non polar	33892256
D-Tartaric acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H](C(=O)O)[C@H](O)C(=O)O	1670.2	Semi standard non polar	33892256
D-Tartaric acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](O)[C@H](O)C(=O)O	1648.3	Semi standard non polar	33892256
D-Tartaric acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)C(=O)O	1926.6	Semi standard non polar	33892256
D-Tartaric acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H](C(=O)O)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O	1947.7	Semi standard non polar	33892256
D-Tartaric acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O	1944.5	Semi standard non polar	33892256
D-Tartaric acid,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](O)[C@H](O)C(=O)O[Si](C)(C)C(C)(C)C	1914.7	Semi standard non polar	33892256
D-Tartaric acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O	2219.8	Semi standard non polar	33892256
D-Tartaric acid,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2201.9	Semi standard non polar	33892256
D-Tartaric acid,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2425.8	Semi standard non polar	33892256

Spectra

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

FDB001110

KNApSAcK ID

Not Available

Chemspider ID

388726

KEGG Compound ID

C02107

BioCyc ID

D-TARTRATE

BiGG ID

Not Available

Wikipedia Link

Tartaric acid

METLIN ID

Not Available

PubChem Compound

439655

PDB ID

TAR

ChEBI ID

15672

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1060801

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. Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1

General function:: Involved in galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity
Specific function:: Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on glycoproteins. Can also play a role in glycosaminoglycan biosynthesis. Substrates include asialo-orosomucoid (ASOR), asialo-fetuin, and asialo-neural cell adhesion molecule. Requires sphingomyelin for activity: stearoyl-sphingomyelin was the most effective, followed by palmitoyl-sphingomyelin and lignoceroyl-sphingomyelin. Activity was demonstrated only for sphingomyelin with a saturated fatty acid and not for that with an unsaturated fatty acid, regardless of the length of the acyl group (By similarity).
Gene Name:: B3GAT1
Uniprot ID:: Q9P2W7
Molecular weight:: 38255.675

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 ]

Enzyme Details

2. Hypoxia-inducible factor 1-alpha inhibitor

General function:: Involved in metal ion binding
Specific function:: Hydroxylates HIF-1 alpha at 'Asp-803' in the C-terminal transactivation domain (CAD). Functions as an oxygen sensor and, under normoxic conditions, the hydroxylation prevents interaction of HIF-1 with transcriptional coactivators including Cbp/p300-interacting transactivator. Involved in transcriptional repression through interaction with HIF1A, VHL and histone deacetylases. Hydroxylates specific Asn residues within ankyrin repeat domains (ARD) of NFKB1, NFKBIA, NOTCH1, ASB4, PPP1R12A and several other ARD-containing proteins. Also hydroxylates Asp and His residues within ARDs of ANK1 and TNKS2, respectively. Negatively regulates NOTCH1 activity, accelerating myogenic differentiation. Positively regulates ASB4 activity, promoting vascular differentiation.
Gene Name:: HIF1AN
Uniprot ID:: Q9NWT6
Molecular weight:: 40285.25

Enzyme Details

3. V-type proton ATPase subunit C 1

General function:: Involved in hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
Specific function:: Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit C is necessary for the assembly of the catalytic sector of the enzyme and is likely to have a specific function in its catalytic activity. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells
Gene Name:: ATP6V1C1
Uniprot ID:: P21283
Molecular weight:: 43941.2

References

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 D-Tartaric acid (HMDB0029878)

MOL for HMDB0029878 (D-Tartaric acid)

3D MOL for HMDB0029878 (D-Tartaric acid)

3D SDF for HMDB0029878 (D-Tartaric acid)

3D-SDF for HMDB0029878 (D-Tartaric acid)

PDB for HMDB0029878 (D-Tartaric acid)

3D PDB for HMDB0029878 (D-Tartaric acid)

SMILES for HMDB0029878 (D-Tartaric acid)

INCHI for HMDB0029878 (D-Tartaric acid)

Structure for HMDB0029878 (D-Tartaric acid)

3D Structure for HMDB0029878 (D-Tartaric acid)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

References

References