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Showing metabocard for Tartronate semialdehyde (HMDB0006938)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-09-11 00:41:42 UTC
Update Date2023-02-21 17:17:23 UTC
HMDB IDHMDB0006938
Secondary Accession Numbers
  • HMDB0006781
  • HMDB06781
  • HMDB06938
Metabolite Identification
Common NameTartronate semialdehyde
DescriptionTartronate semialdehyde, also known as 2-hydroxy-3-oxopropanoate, belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn. Tartronate semialdehyde exists in all living organisms, ranging from bacteria to humans. Tartronate semialdehyde has been detected, but not quantified in, several different foods, such as ginsengs (Panax), deerberries (Vaccinium stamineum), sourdough, prickly pears (Opuntia), and groundcherries (Physalis). This could make tartronate semialdehyde a potential biomarker for the consumption of these foods. Tartronate semialdehyde 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 very few articles have been published on Tartronate semialdehyde.
Structure
Data?1676999843
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0006938 (Tartronate semialdehyde)


  Mrv0541 02231220562D          

  7  6  0  0  0  0            999 V2000
   18.0476  -13.0980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4600  -12.3835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0476  -11.6689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2227  -13.0980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2850  -12.3835    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.4600  -10.9550    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2227  -11.6689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  2  0  0  0  0
  1  2  1  0  0  0  0
  2  5  1  0  0  0  0
  2  3  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  2  0  0  0  0
M  END
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3D MOL for HMDB0006938 (Tartronate semialdehyde)

HMDB0006938
     RDKit          3D
Tartronate semialdehyde
 11 10  0  0  0  0  0  0  0  0999 V2000
   -2.0796    0.4128    1.2542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5238   -0.2410    0.4175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2975    0.2237   -0.3249 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0906    1.4824    0.0838 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7766   -0.7345    0.0274 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6816   -1.9628   -0.2339 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9378   -0.3135    0.6637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8928   -1.2144    0.1582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4761    0.1480   -1.4145 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1308    2.1335   -0.6590 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6523    0.0657    0.0274 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  7 11  1  0
M  END
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3D SDF for HMDB0006938 (Tartronate semialdehyde)


  Mrv0541 02231220562D          

  7  6  0  0  0  0            999 V2000
   18.0476  -13.0980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4600  -12.3835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0476  -11.6689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2227  -13.0980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2850  -12.3835    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.4600  -10.9550    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2227  -11.6689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  2  0  0  0  0
  1  2  1  0  0  0  0
  2  5  1  0  0  0  0
  2  3  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006938

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(C=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H4O4/c4-1-2(5)3(6)7/h1-2,5H,(H,6,7)

> <INCHI_KEY>
QWBAFPFNGRFSFB-UHFFFAOYSA-N

> <FORMULA>
C3H4O4

> <MOLECULAR_WEIGHT>
104.0615

> <EXACT_MASS>
104.010958616

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
8.098472826053765

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-3-oxopropanoic acid

> <ALOGPS_LOGP>
-0.92

> <JCHEM_LOGP>
-1.2048919813333332

> <ALOGPS_LOGS>
0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.672921583739743

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.041917575612961

> <JCHEM_PKA_STRONGEST_BASIC>
-4.499627778811981

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
19.4006

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tartronate semialdehyde

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0006938 (Tartronate semialdehyde)

HMDB0006938
     RDKit          3D
Tartronate semialdehyde
 11 10  0  0  0  0  0  0  0  0999 V2000
   -2.0796    0.4128    1.2542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5238   -0.2410    0.4175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2975    0.2237   -0.3249 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0906    1.4824    0.0838 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7766   -0.7345    0.0274 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6816   -1.9628   -0.2339 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9378   -0.3135    0.6637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8928   -1.2144    0.1582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4761    0.1480   -1.4145 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1308    2.1335   -0.6590 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6523    0.0657    0.0274 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  7 11  1  0
M  END
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PDB for HMDB0006938 (Tartronate semialdehyde)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      33.689 -24.450   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      34.459 -23.116   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      33.689 -21.782   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      32.149 -24.450   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      35.999 -23.116   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      34.459 -20.449   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      32.149 -21.782   0.000  0.00  0.00           O+0
CONECT    1    4    2                                                       
CONECT    2    1    5    3                                                  
CONECT    3    2    6    7                                                  
CONECT    4    1                                                            
CONECT    5    2                                                            
CONECT    6    3                                                            
CONECT    7    3                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0006938 (Tartronate semialdehyde)

COMPND    HMDB0006938
HETATM    1  O1  UNL     1      -2.080   0.413   1.254  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.524  -0.241   0.417  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.297   0.224  -0.325  1.00  0.00           C  
HETATM    4  O2  UNL     1       0.091   1.482   0.084  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.777  -0.734   0.027  1.00  0.00           C  
HETATM    6  O3  UNL     1       0.682  -1.963  -0.234  1.00  0.00           O  
HETATM    7  O4  UNL     1       1.938  -0.313   0.664  1.00  0.00           O  
HETATM    8  H1  UNL     1      -1.893  -1.214   0.158  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.476   0.148  -1.414  1.00  0.00           H  
HETATM   10  H3  UNL     1       0.131   2.134  -0.659  1.00  0.00           H  
HETATM   11  H4  UNL     1       2.652   0.066   0.027  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    5    9
CONECT    4   10
CONECT    5    6    6    7
CONECT    7   11
END
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SMILES for HMDB0006938 (Tartronate semialdehyde)

OC(C=O)C(O)=O
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INCHI for HMDB0006938 (Tartronate semialdehyde)

InChI=1S/C3H4O4/c4-1-2(5)3(6)7/h1-2,5H,(H,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Hydroxy-3-oxopropanoateChEBI
2-Hydroxy-3-oxopropanoic acidGenerator
Tartronic acid semialdehydeGenerator
Hydroxymalonaldehydic acidMeSH, HMDB
Tartronic semialdehydeMeSH, HMDB
Chemical FormulaC3H4O4
Average Molecular Weight104.0615
Monoisotopic Molecular Weight104.010958616
IUPAC Name2-hydroxy-3-oxopropanoic acid
Traditional Nametartronate semialdehyde
CAS Registry NumberNot Available
SMILES
OC(C=O)C(O)=O
InChI Identifier
InChI=1S/C3H4O4/c4-1-2(5)3(6)7/h1-2,5H,(H,6,7)
InChI KeyQWBAFPFNGRFSFB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharides
Alternative Parents
Substituents
  • Alpha-hydroxy acid
  • Hydroxy acid
  • 1,3-dicarbonyl compound
  • Monosaccharide
  • Alpha-hydroxyaldehyde
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Aldehyde
  • Alcohol
  • Carbonyl group
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Route of exposureSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility327 g/LALOGPS
logP-0.92ALOGPS
logP-1.2ChemAxon
logS0.5ALOGPS
pKa (Strongest Acidic)3.04ChemAxon
pKa (Strongest Basic)-4.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity19.4 m³·mol⁻¹ChemAxon
Polarizability8.1 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+120.24331661259
DarkChem[M-H]-112.86831661259
DeepCCS[M+H]+125.05430932474
DeepCCS[M-H]-122.25730932474
DeepCCS[M-2H]-158.67330932474
DeepCCS[M+Na]+133.23630932474
AllCCS[M+H]+127.732859911
AllCCS[M+H-H2O]+123.432859911
AllCCS[M+NH4]+131.732859911
AllCCS[M+Na]+132.932859911
AllCCS[M-H]-119.732859911
AllCCS[M+Na-2H]-123.532859911
AllCCS[M+HCOO]-127.732859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.1.33 minutes32390414
Predicted by Siyang on May 30, 20229.5104 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.1 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid229.3 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid711.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid380.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid78.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid268.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid113.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid281.5 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid313.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)454.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid623.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid76.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid848.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid241.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid331.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate757.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA293.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water413.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Tartronate semialdehydeOC(C=O)C(O)=O2314.6Standard polar33892256
Tartronate semialdehydeOC(C=O)C(O)=O843.9Standard non polar33892256
Tartronate semialdehydeOC(C=O)C(O)=O1046.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Tartronate semialdehyde,1TMS,isomer #1C[Si](C)(C)OC(C=O)C(=O)O1162.9Semi standard non polar33892256
Tartronate semialdehyde,1TMS,isomer #2C[Si](C)(C)OC(=O)C(O)C=O1077.6Semi standard non polar33892256
Tartronate semialdehyde,1TMS,isomer #3C[Si](C)(C)OC=C(O)C(=O)O1212.0Semi standard non polar33892256
Tartronate semialdehyde,2TMS,isomer #1C[Si](C)(C)OC(=O)C(C=O)O[Si](C)(C)C1227.5Semi standard non polar33892256
Tartronate semialdehyde,2TMS,isomer #2C[Si](C)(C)OC=C(O[Si](C)(C)C)C(=O)O1315.1Semi standard non polar33892256
Tartronate semialdehyde,2TMS,isomer #3C[Si](C)(C)OC=C(O)C(=O)O[Si](C)(C)C1287.3Semi standard non polar33892256
Tartronate semialdehyde,3TMS,isomer #1C[Si](C)(C)OC=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1396.4Semi standard non polar33892256
Tartronate semialdehyde,3TMS,isomer #1C[Si](C)(C)OC=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1305.1Standard non polar33892256
Tartronate semialdehyde,3TMS,isomer #1C[Si](C)(C)OC=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1352.9Standard polar33892256
Tartronate semialdehyde,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(C=O)C(=O)O1405.6Semi standard non polar33892256
Tartronate semialdehyde,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C(O)C=O1319.4Semi standard non polar33892256
Tartronate semialdehyde,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC=C(O)C(=O)O1479.3Semi standard non polar33892256
Tartronate semialdehyde,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(C=O)O[Si](C)(C)C(C)(C)C1663.8Semi standard non polar33892256
Tartronate semialdehyde,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC=C(O[Si](C)(C)C(C)(C)C)C(=O)O1788.5Semi standard non polar33892256
Tartronate semialdehyde,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC=C(O)C(=O)O[Si](C)(C)C(C)(C)C1734.8Semi standard non polar33892256
Tartronate semialdehyde,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C1999.0Semi standard non polar33892256
Tartronate semialdehyde,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C1886.9Standard non polar33892256
Tartronate semialdehyde,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C1784.9Standard polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB024155
KNApSAcK IDNot Available
Chemspider ID1090
KEGG Compound IDC01146
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1122
PDB IDNot Available
ChEBI ID16992
Food Biomarker OntologyNot Available
VMH ID2H3OPPAN
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Putative hydroxypyruvate isomerase
General function:
Carbohydrate transport and metabolism
Specific function:
Catalyzes the reversible isomerization between hydroxypyruvate and 2-hydroxy-3-oxopropanoate (also termed tartronate semialdehyde) (By similarity).
Gene Name:
HYI
Uniprot ID:
Q5T013
Molecular weight:
30405.4
Reactions
Hydroxypyruvic acid → Tartronate semialdehydedetails