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Showing metabocard for Hydroxypropanedioic acid (HMDB0035227)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 20:10:47 UTC
Update Date2023-02-21 17:24:42 UTC
HMDB IDHMDB0035227
Secondary Accession Numbers
  • HMDB35227
Metabolite Identification
Common NameHydroxypropanedioic acid
DescriptionHydroxypropanedioic acid, also known as 2-tartronic acid or 2-hydroxymalonate, belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. Hydroxypropanedioic acid has been detected, but not quantified in, potatos (Solanum tuberosum). This could make hydroxypropanedioic acid a potential biomarker for the consumption of these foods. Hydroxypropanedioic acid 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 Hydroxypropanedioic acid.
Structure
Data?1677000282
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035227 (Hydroxypropanedioic acid)

  Mrv1652305062021452D          

  8  7  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  2  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
M  END
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3D MOL for HMDB0035227 (Hydroxypropanedioic acid)

HMDB0035227
     RDKit          3D
Hydroxypropanedioic acid
 12 11  0  0  0  0  0  0  0  0999 V2000
    1.8053   -0.8106   -0.9713 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3142   -0.0805   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0341    0.1683    1.0514 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0246    0.5093   -0.2781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4041    1.2989    0.8166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9829   -0.6119   -0.4509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8025   -1.4286   -1.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0458   -0.7350    0.4143 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4773   -0.5666    1.6150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0853    1.1198   -1.2253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3432    2.2609    0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9424   -1.1240    0.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  8 12  1  0
M  END
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3D SDF for HMDB0035227 (Hydroxypropanedioic acid)

  Mrv1652305062021452D          

  8  7  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  2  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035227

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H4O5/c4-1(2(5)6)3(7)8/h1,4H,(H,5,6)(H,7,8)

> <INCHI_KEY>
ROBFUDYVXSDBQM-UHFFFAOYSA-N

> <FORMULA>
C3H4O5

> <MOLECULAR_WEIGHT>
120.0609

> <EXACT_MASS>
120.005873238

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.960469502826717

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxypropanedioic acid

> <ALOGPS_LOGP>
-1.01

> <JCHEM_LOGP>
-1.0462757289999998

> <ALOGPS_LOGS>
0.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.791393825073156

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.156503841175261

> <JCHEM_PKA_STRONGEST_BASIC>
-4.856106978575348

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
20.326

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.82e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tartronic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0035227 (Hydroxypropanedioic acid)

HMDB0035227
     RDKit          3D
Hydroxypropanedioic acid
 12 11  0  0  0  0  0  0  0  0999 V2000
    1.8053   -0.8106   -0.9713 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3142   -0.0805   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0341    0.1683    1.0514 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0246    0.5093   -0.2781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4041    1.2989    0.8166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9829   -0.6119   -0.4509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8025   -1.4286   -1.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0458   -0.7350    0.4143 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4773   -0.5666    1.6150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0853    1.1198   -1.2253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3432    2.2609    0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9424   -1.1240    0.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  8 12  1  0
M  END
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PDB for HMDB0035227 (Hydroxypropanedioic acid)

HEADER    PROTEIN                                 06-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-20         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.000   2.667   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1                                                            
CONECT    5    2                                                            
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    3                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0035227 (Hydroxypropanedioic acid)

COMPND    HMDB0035227
HETATM    1  O1  UNL     1       1.805  -0.811  -0.971  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.314  -0.080  -0.092  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.034   0.168   1.051  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.025   0.509  -0.278  1.00  0.00           C  
HETATM    5  O3  UNL     1      -0.404   1.299   0.817  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.983  -0.612  -0.451  1.00  0.00           C  
HETATM    7  O4  UNL     1      -0.803  -1.429  -1.388  1.00  0.00           O  
HETATM    8  O5  UNL     1      -2.046  -0.735   0.414  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.477  -0.567   1.615  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.085   1.120  -1.225  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.343   2.261   0.630  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.942  -1.124   0.096  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    6   10
CONECT    5   11
CONECT    6    7    7    8
CONECT    8   12
END
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SMILES for HMDB0035227 (Hydroxypropanedioic acid)

OC(C(O)=O)C(O)=O
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INCHI for HMDB0035227 (Hydroxypropanedioic acid)

InChI=1S/C3H4O5/c4-1(2(5)6)3(7)8/h1,4H,(H,5,6)(H,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-HydroxymalonateChEBI
2-Hydroxymalonic acidChEBI
2-Hydroxypropanedioic acidChEBI
2-Tartronic acidChEBI
Tartronic acidChEBI
Hydroxymalonic acidKegg
2-HydroxypropanedioateGenerator
2-TartronateGenerator
TartronateGenerator
HydroxymalonateGenerator
HydroxypropanedioateGenerator
Hydroxy-malonic acidHMDB
Propanedioic acid, hydroxy- (9ci)HMDB
Tartronic acid, 8ciHMDB
Chemical FormulaC3H4O5
Average Molecular Weight120.0609
Monoisotopic Molecular Weight120.005873238
IUPAC Name2-hydroxypropanedioic acid
Traditional Nametartronic acid
CAS Registry Number80-69-3
SMILES
OC(C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C3H4O5/c4-1(2(5)6)3(7)8/h1,4H,(H,5,6)(H,7,8)
InChI KeyROBFUDYVXSDBQM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassDicarboxylic acids and derivatives
Direct ParentDicarboxylic acids and derivatives
Alternative Parents
Substituents
  • 1,3-dicarbonyl compound
  • Monosaccharide
  • Hydroxy acid
  • Dicarboxylic acid or derivatives
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point156 - 158 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB013880
KNApSAcK IDNot Available
Chemspider ID44
KEGG Compound IDC02287
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHydroxymalonic_acid
METLIN IDNot Available
PubChem Compound45
PDB IDNot Available
ChEBI ID16513
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1499701
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Guerranti R, Pagani R, Neri S, Errico SV, Leoncini R, Marinello E: Inhibition and regulation of rat liver L-threonine dehydrogenase by different fatty acids and their derivatives. Biochim Biophys Acta. 2001 Nov 7;1568(1):45-52. [PubMed:11731084 ]
  2. Jacob J, Grimmer G: [Occurrence of alkyl-hydroxymalonic acids in uropygial gland secretions of birds (author's transl)]. Hoppe Seylers Z Physiol Chem. 1973 Dec;354(12):1648-50. [PubMed:4803853 ]
  3. VEITCH FP, BRIERLEY GP: The quantitative determination of tartronic acid (hydroxymalonic acid) in urine and tissues. Biochim Biophys Acta. 1962 Apr 23;58:567-73. [PubMed:14039995 ]
  4. Knope KE, Kimura H, Yasaka Y, Nakahara M, Andrews MB, Cahill CL: Investigation of in situ oxalate formation from 2,3-pyrazinedicarboxylate under hydrothermal conditions using nuclear magnetic resonance spectroscopy. Inorg Chem. 2012 Mar 19;51(6):3883-90. doi: 10.1021/ic3000944. Epub 2012 Feb 24. [PubMed:22360688 ]
  5. Shen JM, Chen ZL, Xu ZZ, Li XY, Xu BB, Qi F: Kinetics and mechanism of degradation of p-chloronitrobenzene in water by ozonation. J Hazard Mater. 2008 Apr 15;152(3):1325-31. Epub 2007 Aug 8. [PubMed:17889996 ]
  6. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
  7. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details
1. Sulfotransferase family cytosolic 2B member 1
General function:
Involved in sulfotransferase activity
Specific function:
Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs and xenobiotic compounds. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Sulfates hydroxysteroids like DHEA. Isoform 1 preferentially sulfonates cholesterol, and isoform 2 avidly sulfonates pregnenolone but not cholesterol.
Gene Name:
SULT2B1
Uniprot ID:
O00204
Molecular weight:
39598.595
Reactions
Hydroxypropanedioic acid → 2-(sulfooxy)propanedioic aciddetails
Enzyme Details
2. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
Hydroxypropanedioic acid → 2-[(6-carboxy-3,4,5-trihydroxyoxan-2-yl)oxy]propanedioic aciddetails
Hydroxypropanedioic acid → 6-[(2-carboxy-2-hydroxyacetyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic aciddetails
Enzyme Details
3. NADP-dependent malic enzyme, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
ME3
Uniprot ID:
Q16798
Molecular weight:
67067.875
References
  1. 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 ]
  2. 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 ]
  3. 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 ]
Enzyme Details
4. NAD-dependent malic enzyme, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
ME2
Uniprot ID:
P23368
Molecular weight:
53585.73
References
  1. 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 ]
  2. 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 ]