Showing metabocard for L-Arabitol (MMDBc0000202)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:39:36 UTC
Update Date2024-04-30 19:31:28 UTC
Metabolite IDMMDBc0000202
Metabolite Identification
Common NameL-Arabitol
DescriptionL-Arabitol, also known as L-arabinitol or L-lyxitol, is a member of the class of compounds known as sugar alcohols. Sugar alcohols are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone reducing sugar) has been reduced to a primary or secondary hydroxyl group. L-Arabitol is soluble (in water) and is a very weakly acidic compound (based on its pKa). L-Arabitol can be found in a number of food items such as sweet potato, deerberry, moth bean, and European chestnut, which makes L-arabitol a potential biomarker for the consumption of these food products. L-Arabitol can be found in most biofluids, including urine, cerebrospinal fluid (CSF), saliva, and blood. L-Arabitol exists in all living species, ranging from bacteria to humans. Moreover, L-arabitol is found to be associated with Alzheimer's disease and ribose-5-phosphate isomerase deficiency, which is an inborn error of metabolism. L-Arabitol can be formed by the reduction of either arabinose or lyxose. L-Arabitol has been reported in pentosuric acidemia (PMID: 13525419 ). L-Arabinosinuia has been described in a patient, presented at the age of 16 months with delayed motor development and facial dysmorphism (PMID: 12359133 ) Congenital liver cirrhosis has been recently described in a patient with highly elevated plasma and urine levels of arabitol due to transaldolase deficiency (Inherit Metab Dis 23(Suppl. 1):172, 2000).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb706981f8>

ChEBI
  Mrv1652305271900182D          

 10  9  0  0  1  0            999 V2000
    6.9355   -3.2158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2290   -2.7900    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5066   -3.1953    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.8000   -2.7695    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0776   -3.1748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6580   -2.8105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2340   -1.9652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5016   -4.0202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8050   -1.9446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0726   -3.9997    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  2  1  1  0  0  0  0
  2  7  1  1  0  0  0
  3  2  1  0  0  0  0
  3  8  1  1  0  0  0
  4  3  1  0  0  0  0
  4  9  1  6  0  0  0
  5  4  1  0  0  0  0
 10  5  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fdb706981f8>

HMDB0001851
     RDKit          3D
L-Arabitol
 22 21  0  0  0  0  0  0  0  0999 V2000
    2.2703    0.7600   -1.4179 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2187   -0.3029   -0.5092 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3291    0.0973    0.6454 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2758   -0.9567    1.5501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0532    0.4926    0.1700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7873    0.8779    1.2814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7659   -0.6378   -0.5024 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9170   -1.7471    0.3344 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1554   -0.1469   -0.8783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8814    0.2195    0.2601 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0758    1.2933   -1.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2462   -0.4359   -0.1188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8985   -1.2496   -0.9782 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7885    0.9753    1.1420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5266   -0.8015    2.1760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0043    1.3320   -0.5374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5417    1.7639    1.6241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2838   -0.9907   -1.4284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5595   -1.5795    1.0452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0109    0.7553   -1.5135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7444   -0.9367   -1.3960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9332    1.2183    0.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  1
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  6
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
M  END
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3D SDF for #<Metabolite:0x00007fdb706981f8>

ChEBI
  Mrv1652305271900182D          

 10  9  0  0  1  0            999 V2000
    6.9355   -3.2158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2290   -2.7900    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5066   -3.1953    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.8000   -2.7695    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0776   -3.1748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6580   -2.8105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2340   -1.9652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5016   -4.0202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8050   -1.9446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0726   -3.9997    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  2  1  1  0  0  0  0
  2  7  1  1  0  0  0
  3  2  1  0  0  0  0
  3  8  1  1  0  0  0
  4  3  1  0  0  0  0
  4  9  1  6  0  0  0
  5  4  1  0  0  0  0
 10  5  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000202

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4-/m0/s1

> <INCHI_KEY>
HEBKCHPVOIAQTA-IMJSIDKUSA-N

> <FORMULA>
C5H12O5

> <MOLECULAR_WEIGHT>
152.1458

> <EXACT_MASS>
152.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.275101100378855

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4S)-pentane-1,2,3,4,5-pentol

> <ALOGPS_LOGP>
-2.53

> <JCHEM_LOGP>
-3.099683906666666

> <ALOGPS_LOGS>
0.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.742189661908146

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.760078510562963

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9742034412471314

> <JCHEM_POLAR_SURFACE_AREA>
101.15

> <JCHEM_REFRACTIVITY>
32.44109999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.64e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
arabinitol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fdb706981f8>

HMDB0001851
     RDKit          3D
L-Arabitol
 22 21  0  0  0  0  0  0  0  0999 V2000
    2.2703    0.7600   -1.4179 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2187   -0.3029   -0.5092 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3291    0.0973    0.6454 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2758   -0.9567    1.5501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0532    0.4926    0.1700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7873    0.8779    1.2814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7659   -0.6378   -0.5024 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9170   -1.7471    0.3344 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1554   -0.1469   -0.8783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8814    0.2195    0.2601 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0758    1.2933   -1.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2462   -0.4359   -0.1188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8985   -1.2496   -0.9782 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7885    0.9753    1.1420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5266   -0.8015    2.1760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0043    1.3320   -0.5374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5417    1.7639    1.6241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2838   -0.9907   -1.4284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5595   -1.5795    1.0452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0109    0.7553   -1.5135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7444   -0.9367   -1.3960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9332    1.2183    0.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  1
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  6
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
M  END
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PDB for #<Metabolite:0x00007fdb706981f8>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: ChEBI                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      12.946  -6.003   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.627  -5.208   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.279  -5.965   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.960  -5.170   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.612  -5.926   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      14.295  -5.246   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      11.637  -3.668   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      10.270  -7.504   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       8.969  -3.630   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       7.602  -7.466   0.000  0.00  0.00           O+0
CONECT    1    6    2                                                       
CONECT    2    1    7    3                                                  
CONECT    3    2    8    4                                                  
CONECT    4    3    9    5                                                  
CONECT    5    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 #<Metabolite:0x00007fdb706981f8>

COMPND    HMDB0001851
HETATM    1  O1  UNL     1       2.270   0.760  -1.418  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.219  -0.303  -0.509  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.329   0.097   0.645  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.276  -0.957   1.550  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.053   0.493   0.170  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.787   0.878   1.281  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.766  -0.638  -0.502  1.00  0.00           C  
HETATM    8  O4  UNL     1      -0.917  -1.747   0.334  1.00  0.00           O  
HETATM    9  C5  UNL     1      -2.155  -0.147  -0.878  1.00  0.00           C  
HETATM   10  O5  UNL     1      -2.881   0.220   0.260  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.076   1.293  -1.306  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.246  -0.436  -0.119  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.898  -1.250  -0.978  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.789   0.975   1.142  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.527  -0.802   2.176  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.004   1.332  -0.537  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.542   1.764   1.624  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.284  -0.991  -1.428  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.560  -1.579   1.045  1.00  0.00           H  
HETATM   20  H10 UNL     1      -2.011   0.755  -1.513  1.00  0.00           H  
HETATM   21  H11 UNL     1      -2.744  -0.937  -1.396  1.00  0.00           H  
HETATM   22  H12 UNL     1      -2.933   1.218   0.357  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    5   14
CONECT    4   15
CONECT    5    6    7   16
CONECT    6   17
CONECT    7    8    9   18
CONECT    8   19
CONECT    9   10   20   21
CONECT   10   22
END
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SMILES for #<Metabolite:0x00007fdb706981f8>

OC[C@H](O)C(O)[C@@H](O)CO
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INCHI for #<Metabolite:0x00007fdb706981f8>

InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4-/m0/s1
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Synonyms
ValueSource
L-ArabinolChEBI
L-LyxitolChEBI
L-ArabinitolKegg
Arabitol, (D)-isomerHMDB
D-ArabinitolHMDB
D-ArabitolHMDB
DL-ArabitolHMDB
Arabino-pentitolHMDB
ArabitolHMDB
(+--)-ArabitolHMDB
Arabitol, (L)-isomerHMDB
LyxitolHMDB
L(-)-ArabitolHMDB
1,2,3,4,5-PentahydroxypentaneHMDB
Adonite adonitolHMDB
ArabinitolHMDB
L-(+)-ArabitolHMDB
L-(-)-ArabinitolHMDB
L-(-)-ArabitolHMDB
L-ArabitolChEBI
Molecular FormulaC5H12O5
Average Mass152.1458
Monoisotopic Mass152.068473494
IUPAC Name(2S,4S)-pentane-1,2,3,4,5-pentol
Traditional Namearabinitol
CAS Registry Number7643-75-6
SMILES
OC[C@H](O)C(O)[C@@H](O)CO
InChI Identifier
InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4-/m0/s1
InChI KeyHEBKCHPVOIAQTA-IMJSIDKUSA-N