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Showing metabocard for L-Lyxonic acid (HMDB0060255)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2013-05-09 21:13:47 UTC
Update Date2022-03-07 03:17:42 UTC
HMDB IDHMDB0060255
Secondary Accession Numbers
  • HMDB60255
Metabolite Identification
Common NameL-Lyxonic acid
DescriptionL-Lyxonic acid, also known as L-lyxonate, 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. L-Lyxonic 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 L-Lyxonic acid.
Structure
Data?1563866036
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060255 (L-Lyxonic acid)

  Mrv1652307171917502D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8  9  1  6  0  0  0
  6  7  1  6  0  0  0
  4  5  1  1  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
Download

3D MOL for HMDB0060255 (L-Lyxonic acid)

HMDB0060255
     RDKit          3D
L-Lyxonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    3.4193    0.3861   -0.9996 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5516   -0.2069   -0.2806 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9620   -0.6102    0.9804 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1731   -0.4557   -0.7618 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0125    0.0419   -2.0513 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1305    0.1693    0.1707 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2949   -0.3309    1.4583 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2179   -0.2650   -0.3299 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2328   -1.6610   -0.3252 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3529    0.2985    0.4682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2905    1.6848    0.4301 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1734    0.0809    1.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0292   -1.5555   -0.8033 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7535    0.6516   -2.2793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2664    1.2550    0.1902 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4365    0.3879    2.1241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3350    0.0815   -1.3791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2808   -2.0355    0.5748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3953   -0.0876    1.4993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2959   -0.0114   -0.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8019    2.0653   -0.3327 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  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  1
  7 16  1  0
  8 17  1  6
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
Download

3D SDF for HMDB0060255 (L-Lyxonic acid)

  Mrv1652307171917502D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8  9  1  6  0  0  0
  6  7  1  6  0  0  0
  4  5  1  1  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060255

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H](O)[C@@H](O)[C@@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4+/m0/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-PZGQECOJSA-N

> <FORMULA>
C5H10O6

> <MOLECULAR_WEIGHT>
166.129

> <EXACT_MASS>
166.047738042

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.365565921918606

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid

> <ALOGPS_LOGP>
-2.48

> <JCHEM_LOGP>
-2.7794093686666668

> <ALOGPS_LOGS>
0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.768659694136133

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.393139811550542

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974562302797298

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
32.3085

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0060255 (L-Lyxonic acid)

HMDB0060255
     RDKit          3D
L-Lyxonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    3.4193    0.3861   -0.9996 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5516   -0.2069   -0.2806 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9620   -0.6102    0.9804 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1731   -0.4557   -0.7618 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0125    0.0419   -2.0513 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1305    0.1693    0.1707 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2949   -0.3309    1.4583 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2179   -0.2650   -0.3299 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2328   -1.6610   -0.3252 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3529    0.2985    0.4682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2905    1.6848    0.4301 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1734    0.0809    1.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0292   -1.5555   -0.8033 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7535    0.6516   -2.2793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2664    1.2550    0.1902 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4365    0.3879    2.1241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3350    0.0815   -1.3791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2808   -2.0355    0.5748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3953   -0.0876    1.4993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2959   -0.0114   -0.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8019    2.0653   -0.3327 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  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  1
  7 16  1  0
  8 17  1  6
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
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PDB for HMDB0060255 (L-Lyxonic acid)

HEADER    PROTEIN                                 17-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUL-19         0                                  
HETATM    1  C   UNK     0      -6.500   0.395   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -7.833  -0.375   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -6.500   1.935   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -5.166  -0.375   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -5.166  -1.915   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -3.832   0.395   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.832   1.935   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.499  -0.375   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.499  -1.915   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.165   0.395   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.169  -0.375   0.000  0.00  0.00           O+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4    8    7                                                  
CONECT    7    6                                                            
CONECT    8    6   10    9                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0060255 (L-Lyxonic acid)

COMPND    HMDB0060255
HETATM    1  O1  UNL     1       3.419   0.386  -1.000  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.552  -0.207  -0.281  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.962  -0.610   0.980  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.173  -0.456  -0.762  1.00  0.00           C  
HETATM    5  O3  UNL     1       1.013   0.042  -2.051  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.130   0.169   0.171  1.00  0.00           C  
HETATM    7  O4  UNL     1       0.295  -0.331   1.458  1.00  0.00           O  
HETATM    8  C4  UNL     1      -1.218  -0.265  -0.330  1.00  0.00           C  
HETATM    9  O5  UNL     1      -1.233  -1.661  -0.325  1.00  0.00           O  
HETATM   10  C5  UNL     1      -2.353   0.298   0.468  1.00  0.00           C  
HETATM   11  O6  UNL     1      -2.290   1.685   0.430  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.173   0.081   1.674  1.00  0.00           H  
HETATM   13  H2  UNL     1       1.029  -1.555  -0.803  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.754   0.652  -2.279  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.266   1.255   0.190  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.436   0.388   2.124  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.335   0.081  -1.379  1.00  0.00           H  
HETATM   18  H7  UNL     1      -1.281  -2.035   0.575  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.395  -0.088   1.499  1.00  0.00           H  
HETATM   20  H9  UNL     1      -3.296  -0.011  -0.027  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.802   2.065  -0.333  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    6   13
CONECT    5   14
CONECT    6    7    8   15
CONECT    7   16
CONECT    8    9   10   17
CONECT    9   18
CONECT   10   11   19   20
CONECT   11   21
END
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SMILES for HMDB0060255 (L-Lyxonic acid)

OC[C@H](O)[C@@H](O)[C@@H](O)C(O)=O
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INCHI for HMDB0060255 (L-Lyxonic acid)

InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4+/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(2R,3R,4S)-2,3,4,5-Tetrahydroxypentanoic acidChEBI
(2R,3R,4S)-2,3,4,5-TetrahydroxypentanoateGenerator
L-LyxonateGenerator
​L-​lyxonateHMDB
2,3,4,5-Tetrahydroxypentanoic acidHMDB
LyxonateHMDB
Lyxonic acidHMDB
L-Lyxonic acidKEGG
Chemical FormulaC5H10O6
Average Molecular Weight166.129
Monoisotopic Molecular Weight166.047738042
IUPAC Name(2R,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid
Traditional Name(2R,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid
CAS Registry Number4172-43-4
SMILES
OC[C@H](O)[C@@H](O)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4+/m0/s1
InChI KeyQXKAIJAYHKCRRA-PZGQECOJSA-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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar acids and derivatives
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Beta-hydroxy acid
  • Sugar acid
  • Short-chain hydroxy acid
  • Alpha-hydroxy acid
  • Fatty acid
  • Hydroxy acid
  • Monosaccharide
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Polyol
  • Primary alcohol
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID559150
KEGG Compound IDC05412
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkXylonic acid
METLIN IDNot Available
PubChem Compound644110
PDB IDNot Available
ChEBI ID6268
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. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]