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Showing metabocard for (2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal (HMDB0242608)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-01 22:43:01 UTC
Update Date2021-09-26 22:50:10 UTC
HMDB IDHMDB0242608
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal
Description(2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal, also known as methoxypectin or pectinic acid, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms (2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal exists in all living organisms, ranging from bacteria to humans (2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal is found, on average, in the highest concentration within flaxseeds (Linum usitatissimum) (2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal has also been detected, but not quantified in, cocoa beans (Theobroma cacao). This could make (2R,3R,4R)-2,3,4,5-tetrahydroxypentanal a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on (2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal. This compound has been identified in human blood as reported by (PMID: 31557052 ). (2r,3r,4r)-2,3,4,5-tetrahydroxypentanal is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0242608 ((2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal)

Structure #1
  Mrv0541 02241207092D          

 10  9  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
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  6  2  0  0  0  0
  2  4  1  0  0  0  0
  2  7  1  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  1  0  0  0  0
M  END
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3D MOL for HMDB0242608 ((2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal)

HMDB0246927
     RDKit          3D
L-(+)-Arabinose
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.7823    0.7609    1.2531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1711    0.8022    0.2044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6261   -0.4514   -0.3442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9434   -1.4915    0.5054 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1492   -0.3831   -0.6367 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1311    0.6761   -1.4941 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6791   -0.3015    0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4071    0.8913    1.3012 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1504   -0.3501    0.2751 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4818    0.7266   -0.5423 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0692    1.7774   -0.2605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1704   -0.6295   -1.3177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7631   -1.9790    0.2561 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1179   -1.3167   -1.1744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3055    1.5100   -1.2597 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4808   -1.1170    1.3216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9887    1.6304    1.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3200   -1.2697   -0.3612 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7928   -0.4616    1.1457 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4304    0.9762   -0.4977 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  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
M  END
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3D SDF for HMDB0242608 ((2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal)

Structure #1
  Mrv0541 02241207092D          

 10  9  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
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  6  2  0  0  0  0
  2  4  1  0  0  0  0
  2  7  1  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0242608

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2

> <INCHI_KEY>
PYMYPHUHKUWMLA-UHFFFAOYSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.448565428033513

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4,5-tetrahydroxypentanal

> <ALOGPS_LOGP>
-2.28

> <JCHEM_LOGP>
-2.9380256209999995

> <ALOGPS_LOGS>
0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.05193577352083

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.871096474968176

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9744929158468105

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
31.383099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.80e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(+)-xylose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0242608 ((2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal)

HMDB0246927
     RDKit          3D
L-(+)-Arabinose
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.7823    0.7609    1.2531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1711    0.8022    0.2044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6261   -0.4514   -0.3442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9434   -1.4915    0.5054 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1492   -0.3831   -0.6367 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1311    0.6761   -1.4941 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6791   -0.3015    0.6269 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4071    0.8913    1.3012 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1504   -0.3501    0.2751 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4818    0.7266   -0.5423 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0692    1.7774   -0.2605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1704   -0.6295   -1.3177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7631   -1.9790    0.2561 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1179   -1.3167   -1.1744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3055    1.5100   -1.2597 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4808   -1.1170    1.3216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9887    1.6304    1.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3200   -1.2697   -0.3612 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7928   -0.4616    1.1457 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4304    0.9762   -0.4977 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  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
M  END
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PDB for HMDB0242608 ((2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.025   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.976   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.691   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.357   1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.644   2.104   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.358   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.976   3.644   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.691   3.644   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.357  -0.206   0.000  0.00  0.00           O+0
CONECT    1    3    6                                                       
CONECT    2    4    7                                                       
CONECT    3    1    5    8                                                  
CONECT    4    2    5    9                                                  
CONECT    5    3    4   10                                                  
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0242608 ((2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal)

COMPND    HMDB0242608
HETATM    1  O1  UNL     1      -2.686  -0.537  -1.675  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.506  -0.542  -1.431  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.001  -1.232  -0.235  1.00  0.00           C  
HETATM    4  O2  UNL     1      -2.132  -1.807   0.403  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.415  -0.261   0.743  1.00  0.00           C  
HETATM    6  O3  UNL     1      -1.372   0.712   1.023  1.00  0.00           O  
HETATM    7  C4  UNL     1       0.941   0.241   0.497  1.00  0.00           C  
HETATM    8  O4  UNL     1       1.846  -0.791   0.218  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.156   1.352  -0.456  1.00  0.00           C  
HETATM   10  O5  UNL     1       2.496   1.787  -0.253  1.00  0.00           O  
HETATM   11  H1  UNL     1      -0.831  -0.039  -2.093  1.00  0.00           H  
HETATM   12  H2  UNL     1      -0.338  -2.086  -0.460  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.554  -1.049   0.890  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.355  -0.838   1.728  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.091   1.622   0.816  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.310   0.632   1.504  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.730  -1.484   0.930  1.00  0.00           H  
HETATM   18  H8  UNL     1       1.171   1.085  -1.530  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.521   2.232  -0.273  1.00  0.00           H  
HETATM   20  H10 UNL     1       3.109   1.003  -0.347  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   11
CONECT    3    4    5   12
CONECT    4   13
CONECT    5    6    7   14
CONECT    6   15
CONECT    7    8    9   16
CONECT    8   17
CONECT    9   10   18   19
CONECT   10   20
END
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SMILES for HMDB0242608 ((2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal)

OCC(O)C(O)C(O)C=O
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INCHI for HMDB0242608 ((2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal)

InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
MethoxypectinHMDB
Pectinic acidHMDB
Calcium pectinateHMDB
PectinHMDB
Methoxy pectinHMDB
MethoxylpectinHMDB
Zinc pectinateHMDB
Pectin, methoxyHMDB
Pectinate, calciumHMDB
Pectinate, zincHMDB
PectinsHMDB
Citrus pectinHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name2,3,4,5-tetrahydroxypentanal
Traditional Name(+)-xylose
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)C(O)C=O
InChI Identifier
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2
InChI KeyPYMYPHUHKUWMLA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Beta-hydroxy aldehyde
  • Alpha-hydroxyaldehyde
  • Secondary alcohol
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Primary alcohol
  • Carbonyl group
  • Aldehyde
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB005965
KNApSAcK IDNot Available
Chemspider ID831
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPentose
METLIN IDNot Available
PubChem Compound854
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]