Np mrd loader

Showing NP-Card for L-Arabitol (NP0000235)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version1.0
Created at2006-02-16 09:36:44 UTC
Updated at2021-08-19 23:57:58 UTC
NP-MRD IDNP0000235
Secondary Accession NumbersNone
Natural Product 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. 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000235 (L-Arabitol)

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
Download

3D MOL for NP0000235 (L-Arabitol)

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
Download

3D SDF for NP0000235 (L-Arabitol)

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>
NP0000235

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000235 (L-Arabitol)

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
Download

PDB for NP0000235 (L-Arabitol)

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
Download

3D PDB for NP0000235 (L-Arabitol)

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
Download

SMILES for NP0000235 (L-Arabitol)

OC[C@H](O)C(O)[C@@H](O)CO
Download

INCHI for NP0000235 (L-Arabitol)

InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4-/m0/s1
Download
View in JSmol
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
Chemical FormulaC5H12O5
Average Mass152.1458 Da
Monoisotopic Mass152.06847 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Adonis vernalisLOTUS Database
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar alcohols. These 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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar alcohols
Alternative Parents
Substituents
  • Sugar alcohol
  • Monosaccharide
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point101 - 104 °CNot Available
Boiling Point494.53 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-2.649 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility664 g/LALOGPS
logP-2.5ALOGPS
logP-3.1ChemAxon
logS0.64ALOGPS
pKa (Strongest Acidic)12.76ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area101.15 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.44 m³·mol⁻¹ChemAxon
Polarizability14.28 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001851
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022709
KNApSAcK IDNot Available
Chemspider ID388391
KEGG Compound IDC00532
BioCyc IDL-ARABITOL
BiGG ID35268
Wikipedia LinkArabitol
METLIN ID141
PubChem Compound439255
PDB IDNot Available
ChEBI ID18403
Good Scents IDrw1253351
References
General References
  1. Onkenhout W, Groener JE, Verhoeven NM, Yin C, Laan LA: L-Arabinosuria: a new defect in human pentose metabolism. Mol Genet Metab. 2002 Sep-Oct;77(1-2):80-5. [PubMed:12359133 ]
  2. TOUSTER O, HARWELL SO: The isolation of L-arabitol from pentosuric urine. J Biol Chem. 1958 Feb;230(2):1031-41. [PubMed:13525419 ]
  3. Sreenath K, Venkatesh YP: Reductively aminated D-xylose-albumin conjugate as the immunogen for generation of IgG and IgE antibodies specific to D-xylitol, a haptenic allergen. Bioconjug Chem. 2007 Nov-Dec;18(6):1995-2003. doi: 10.1021/bc700175g. Epub 2007 Nov 3. [PubMed:17979222 ]
  4. Mach-Aigner AR, Gudynaite-Savitch L, Mach RL: L-arabitol is the actual inducer of xylanase expression in Hypocrea jecorina (Trichoderma reesei). Appl Environ Microbiol. 2011 Sep;77(17):5988-94. doi: 10.1128/AEM.05427-11. Epub 2011 Jul 8. [PubMed:21742908 ]
  5. Sakakibara Y, Torigoe K: Biochemical characterization of l-arabitol 2-dehydrogenase from Pantoea ananatis. J Biosci Bioeng. 2012 Jun;113(6):715-8. doi: 10.1016/j.jbiosc.2012.01.008. Epub 2012 Feb 4. [PubMed:22306314 ]