Showing metabocard for D-Arabitol (MMDBc0000116)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:36:27 UTC
Update Date2024-04-30 19:31:06 UTC
Metabolite IDMMDBc0000116
Metabolite Identification
Common NameD-Arabitol
DescriptionD-Arabitol is a polyol. Polyols are sugar alcohols linked to the pentose phosphate pathway (PPP). They are classified on the basis of the number of carbon atoms. Polyols occur in body fluids. A patient with leukoencephalopathy and peripheral neuropathy has been identified as suffering from ribose-5-phosphate isomerase (RPI) deficiency, a defect in the PPP. In this disorder, highly elevated concentrations of the C5 polyols such as D-arabitol are found in body fluids. In addition, transaldolase deficiency, another defect in the PPP, has been diagnosed in a patient with mainly liver problems among others. This patient had increased concentrations of polyols, mainly D-arabitol. So far, the pathophysiological role of polyols is relatively unknown. It is thought that D-arabitol is a metabolic end-product in humans. The strong brain-CSF-plasma gradient of polyols in the patient with RPI deficiency suggested a primary metabolic disorder. The mechanisms of brain and neuronal damage in RPI deficiency remain to be elucidated. A neurotoxic effect due to the accumulation of the polyols may play a role. D-Arabitol is a product of the enzyme D-arabinitol 4-dehydrogenase (EC 1.1.1.11) in the pentose and glucuronate interconversion pathway (PMID: 16435225 , J Inherit Metab Dis. 2005;28(6):1181-3). D-Arabitol has also been found to be a fungal metabolite, urinary D-Arabinitol is a marker for invasive candidiasis or infection by Candida fungal species (PMID: 15183861 ; PMID: 10647119 ). It can also a metabolite in Debaryomyces, Pichia and Zygosaccharomyces (PMID: 25809659 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9233c23270>

ChEBI
  Mrv1652306232021442D          

 10  9  0  0  1  0            999 V2000
    4.4922   -3.0367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2019   -3.4570    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.9211   -3.0462    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.6310   -3.4664    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.3502   -3.0557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7729   -3.4475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2033   -4.2818    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9197   -2.2212    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6324   -4.2912    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3488   -2.2307    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  6  0  0  0
  3  2  1  0  0  0  0
  3  8  1  6  0  0  0
  4  3  1  0  0  0  0
  4  9  1  1  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:0x00007f9233c23270>

HMDB0000568
     RDKit          3D
D-Arabitol
 22 21  0  0  0  0  0  0  0  0999 V2000
    2.8495    0.9305    0.7642 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8469   -0.0417    0.5669 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8877    0.5227   -0.4358 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6227    0.7679   -1.6120 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2345   -0.3865   -0.7981 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3332   -1.5687   -1.3102 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1411   -0.7736    0.3094 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1188   -1.6297   -0.2591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9055    0.3745    0.9127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1286    1.3222    1.5180 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0210    1.4536   -0.0561 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3571   -0.9528    0.2503 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3839   -0.1852    1.5703 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5668    1.5170   -0.0776 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3656    0.1609   -2.3344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8149    0.0752   -1.6076 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6729   -2.1284   -0.5501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6490   -1.3886    1.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4518   -1.1063   -1.0560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5666    0.8762    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5994   -0.0828    1.6777 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2972    2.2435    1.2602 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  1
  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:0x00007f9233c23270>

ChEBI
  Mrv1652306232021442D          

 10  9  0  0  1  0            999 V2000
    4.4922   -3.0367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2019   -3.4570    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.9211   -3.0462    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.6310   -3.4664    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.3502   -3.0557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7729   -3.4475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2033   -4.2818    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9197   -2.2212    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6324   -4.2912    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3488   -2.2307    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  6  0  0  0
  3  2  1  0  0  0  0
  3  8  1  6  0  0  0
  4  3  1  0  0  0  0
  4  9  1  1  0  0  0
  5  4  1  0  0  0  0
 10  5  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000116

> <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-/m1/s1

> <INCHI_KEY>
HEBKCHPVOIAQTA-QWWZWVQMSA-N

> <FORMULA>
C5H12O5

> <MOLECULAR_WEIGHT>
152.1458

> <EXACT_MASS>
152.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.277797496387443

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,4R)-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>
arabitol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9233c23270>

HMDB0000568
     RDKit          3D
D-Arabitol
 22 21  0  0  0  0  0  0  0  0999 V2000
    2.8495    0.9305    0.7642 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8469   -0.0417    0.5669 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8877    0.5227   -0.4358 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6227    0.7679   -1.6120 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2345   -0.3865   -0.7981 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3332   -1.5687   -1.3102 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1411   -0.7736    0.3094 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1188   -1.6297   -0.2591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9055    0.3745    0.9127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1286    1.3222    1.5180 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0210    1.4536   -0.0561 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3571   -0.9528    0.2503 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3839   -0.1852    1.5703 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5668    1.5170   -0.0776 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3656    0.1609   -2.3344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8149    0.0752   -1.6076 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6729   -2.1284   -0.5501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6490   -1.3886    1.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4518   -1.1063   -1.0560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5666    0.8762    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5994   -0.0828    1.6777 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2972    2.2435    1.2602 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  1
  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:0x00007f9233c23270>

HEADER    PROTEIN                                 23-JUN-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: ChEBI                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-JUN-20         0                                  
HETATM    1  C   UNK     0       8.385  -5.669   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.710  -6.453   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.053  -5.686   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.378  -6.471   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.720  -5.704   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       7.043  -6.435   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       9.713  -7.993   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      11.050  -4.146   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      12.380  -8.010   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      13.718  -4.164   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:0x00007f9233c23270>

COMPND    HMDB0000568
HETATM    1  O1  UNL     1       2.849   0.930   0.764  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.847  -0.042   0.567  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.888   0.523  -0.436  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.623   0.768  -1.612  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.234  -0.386  -0.798  1.00  0.00           C  
HETATM    6  O3  UNL     1       0.333  -1.569  -1.310  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.141  -0.774   0.309  1.00  0.00           C  
HETATM    8  O4  UNL     1      -2.119  -1.630  -0.259  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.905   0.375   0.913  1.00  0.00           C  
HETATM   10  O5  UNL     1      -1.129   1.322   1.518  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.021   1.454  -0.056  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.357  -0.953   0.250  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.384  -0.185   1.570  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.567   1.517  -0.078  1.00  0.00           H  
HETATM   15  H5  UNL     1       1.366   0.161  -2.334  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.815   0.075  -1.608  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.673  -2.128  -0.550  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.649  -1.389   1.089  1.00  0.00           H  
HETATM   19  H9  UNL     1      -2.452  -1.106  -1.056  1.00  0.00           H  
HETATM   20  H10 UNL     1      -2.567   0.876   0.178  1.00  0.00           H  
HETATM   21  H11 UNL     1      -2.599  -0.083   1.678  1.00  0.00           H  
HETATM   22  H12 UNL     1      -1.297   2.244   1.260  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:0x00007f9233c23270>

OC[C@@H](O)C(O)[C@H](O)CO
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INCHI for #<Metabolite:0x00007f9233c23270>

InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4-/m1/s1
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Synonyms
ValueSource
D-ArabinolChEBI
D-LyxitolChEBI
D-ArabinitolKegg
Arabitol, (D)-isomerHMDB
ArabitolHMDB
D-(+)-ArabitolHMDB
(+--)-ArabitolHMDB
DL-ArabitolHMDB
Arabino-pentitolHMDB
LyxitolHMDB
D-ArabitolChEBI
Molecular FormulaC5H12O5
Average Mass152.1458
Monoisotopic Mass152.068473494
IUPAC Name(2R,4R)-pentane-1,2,3,4,5-pentol
Traditional Namearabitol
CAS Registry Number488-82-4
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-/m1/s1
InChI KeyHEBKCHPVOIAQTA-QWWZWVQMSA-N