Showing NP-Card for D-Arabitol (NP0000594)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2024-09-17 15:42:21 UTC
NP-MRD IDNP0000594
Secondary Accession NumbersNone
Natural Product 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).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000594 (D-Arabitol)

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
Download

3D MOL for NP0000594 (D-Arabitol)

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
Download

3D SDF for NP0000594 (D-Arabitol)

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>
NP0000594

> <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-/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

$$$$
Download

3D-SDF for NP0000594 (D-Arabitol)

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
Download

PDB for NP0000594 (D-Arabitol)

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 NP0000594 (D-Arabitol)

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 NP0000594 (D-Arabitol)

OC[C@@H](O)C(O)[C@H](O)CO
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INCHI for NP0000594 (D-Arabitol)

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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View in JSmolView NMR Assignments
Synonyms
ValueSource
D-ArabinolChEBI
D-LyxitolChEBI
D-ArabinitolKegg
Arabitol, (D)-isomerHMDB
ArabitolHMDB
D-(+)-ArabitolHMDB
(+--)-ArabitolHMDB
DL-ArabitolHMDB
Arabino-pentitolHMDB
LyxitolHMDB
D-ArabitolChEBI
Chemical FormulaC5H12O5
Average Mass152.1458 Da
Monoisotopic Mass152.06847 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
Phoma medicaginisKNApSAcK Database
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 Solubility729 mg/mLNot Available
LogP-3.774 (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 IDHMDB0000568
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB001475
KNApSAcK IDC00052193
Chemspider ID84971
KEGG Compound IDC01904
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkD-arabinitol
METLIN ID5551
PubChem Compound94154
PDB IDNot Available
ChEBI ID18333
Good Scents IDrw1233671
References
General References
  1. Kiehn TE, Bernard EM, Gold JW, Armstrong D: Candidiasis: detection by gas-liquid chromatography of D-arabinitol, a fungal metabolite, in human serum. Science. 1979 Nov 2;206(4418):577-80. [PubMed:493963 ]
  2. Klusmann A, Fleischer W, Waldhaus A, Siebler M, Mayatepek E: Influence of D-arabitol and ribitol on neuronal network activity. J Inherit Metab Dis. 2005;28(6):1181-3. [PubMed:16435225 ]
  3. Christensson B, Sigmundsdottir G, Larsson L: D-arabinitol--a marker for invasive candidiasis. Med Mycol. 1999 Dec;37(6):391-6. doi: 10.1046/j.1365-280x.1999.00249.x. [PubMed:10647119 ]
  4. Kordowska-Wiater M: Production of arabitol by yeasts: current status and future prospects. J Appl Microbiol. 2015 Aug;119(2):303-14. doi: 10.1111/jam.12807. Epub 2015 Apr 8. [PubMed:25809659 ]