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Showing NP-Card for D-Threitol (NP0001405)

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Record Information
Version1.0
Created at2006-08-13 12:46:02 UTC
Updated at2021-06-29 00:47:52 UTC
NP-MRD IDNP0001405
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Threitol
DescriptionD-Threitol can be regarded as the main end product of D-xylose metabolism in hummans. Threitol is a C4-polyol (tetritol); the total C4-polyol concentration of threitol decreases with age. Several inborn errors of metabolism with abnormal polyol concentrations in body fluids are known to date (such as pentosuria and galactosemia). Most of these defects can be diagnosed by the assessment of urinary concentrations of polyols. Several studies have revealed that urinary levels of some polyols may vary in diseases associated with carbohydrate metabolism derangements such as diabetes mellitus and uremia. The abnormal occurrence of various polyols in diseases with a specific enzyme deficiency such as pentosuria and galactosemia has also been reported (PMID: 908147 , 16435188 , 14988808 ). Moreover, D-Threitol is found to be associated with ribose-5-phosphate isomerase deficiency, which is also an inborn error of metabolism. Threitol in the urine is a biomarker for the consumption of apples and other fruits.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001405 (D-Threitol)


  Mrv1652307301920082D          

  8  7  0  0  1  0            999 V2000
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  1  6  0  0  0
  2  7  1  6  0  0  0
  1  8  1  0  0  0  0
M  END
Download

3D MOL for NP0001405 (D-Threitol)

HMDB0004136
     RDKit          3D
D-Threitol
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.9603   -0.5637    0.6792 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9507    0.2778    0.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7153   -0.5673    0.0292 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3401   -1.1631    1.2410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4612    0.2969   -0.4358 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7218    1.2509    0.5131 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6165   -0.6640   -0.6588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7666   -0.0479   -1.0744 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6929   -1.5085    0.6808 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2139    0.7734   -0.7154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7246    1.0149    1.0453 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8571   -1.3424   -0.7273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2364   -0.5232    1.7262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1505    0.7811   -1.3825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6155    1.1993    0.9111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8350   -1.2468    0.2576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2408   -1.4145   -1.4040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8106    0.9095   -0.9103 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
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  6
  4 13  1  0
  5 14  1  6
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
M  END
Download

3D SDF for NP0001405 (D-Threitol)


  Mrv1652307301920082D          

  8  7  0  0  1  0            999 V2000
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  1  6  0  0  0
  2  7  1  6  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001405

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H10O4/c5-1-3(7)4(8)2-6/h3-8H,1-2H2/t3-,4-/m1/s1

> <INCHI_KEY>
UNXHWFMMPAWVPI-QWWZWVQMSA-N

> <FORMULA>
C4H10O4

> <MOLECULAR_WEIGHT>
122.1198

> <EXACT_MASS>
122.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
11.663684495732259

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-butane-1,2,3,4-tetrol

> <JCHEM_LOGP>
-2.4693489646666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.285181811808233

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.044993073077713

> <JCHEM_PKA_STRONGEST_BASIC>
-2.973906601202132

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
26.4786

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(-)-threitol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001405 (D-Threitol)

HMDB0004136
     RDKit          3D
D-Threitol
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.9603   -0.5637    0.6792 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9507    0.2778    0.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7153   -0.5673    0.0292 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3401   -1.1631    1.2410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4612    0.2969   -0.4358 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7218    1.2509    0.5131 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6165   -0.6640   -0.6588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7666   -0.0479   -1.0744 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6929   -1.5085    0.6808 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2139    0.7734   -0.7154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7246    1.0149    1.0453 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8571   -1.3424   -0.7273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2364   -0.5232    1.7262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1505    0.7811   -1.3825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6155    1.1993    0.9111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8350   -1.2468    0.2576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2408   -1.4145   -1.4040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8106    0.9095   -0.9103 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
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  6
  4 13  1  0
  5 14  1  6
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
M  END
Download

PDB for NP0001405 (D-Threitol)

HEADER    PROTEIN                                 30-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-19         0                                  
HETATM    1  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.310  -0.206   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3                                                            
CONECT    7    2                                                            
CONECT    8    1                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for NP0001405 (D-Threitol)

COMPND    HMDB0004136
HETATM    1  O1  UNL     1       2.960  -0.564   0.679  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.951   0.278   0.225  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.715  -0.567   0.029  1.00  0.00           C  
HETATM    4  O2  UNL     1       0.340  -1.163   1.241  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.461   0.297  -0.436  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.722   1.251   0.513  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.617  -0.664  -0.659  1.00  0.00           C  
HETATM    8  O4  UNL     1      -2.767  -0.048  -1.074  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.693  -1.508   0.681  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.214   0.773  -0.715  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.725   1.015   1.045  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.857  -1.342  -0.727  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.236  -0.523   1.726  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.150   0.781  -1.383  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.616   1.199   0.911  1.00  0.00           H  
HETATM   16  H8  UNL     1      -1.835  -1.247   0.258  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.241  -1.415  -1.404  1.00  0.00           H  
HETATM   18  H10 UNL     1      -2.811   0.909  -0.910  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3   10   11
CONECT    3    4    5   12
CONECT    4   13
CONECT    5    6    7   14
CONECT    6   15
CONECT    7    8   16   17
CONECT    8   18
END
Download

SMILES for NP0001405 (D-Threitol)

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

INCHI for NP0001405 (D-Threitol)

InChI=1S/C4H10O4/c5-1-3(7)4(8)2-6/h3-8H,1-2H2/t3-,4-/m1/s1
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View in JSmol
Synonyms
ValueSource
D-Threo-tetritolChEBI
(-)-ThreitolHMDB
(R*,r*)-1,2,3,4-butanetetrolHMDB
ThreitHMDB
ThreitolHMDB
Threitol, ((r*,r*)-(+-))-isomerHMDB
Threitol, (R-(r*,r*))-isomerHMDB
1,2,3,4-TetrahydroxybutaneHMDB
Chemical FormulaC4H10O4
Average Mass122.1198 Da
Monoisotopic Mass122.05791 Da
IUPAC Name(2R,3R)-butane-1,2,3,4-tetrol
Traditional Name(-)-threitol
CAS Registry Number2418-52-2
SMILES
OC[C@@H](O)[C@H](O)CO
InChI Identifier
InChI=1S/C4H10O4/c5-1-3(7)4(8)2-6/h3-8H,1-2H2/t3-,4-/m1/s1
InChI KeyUNXHWFMMPAWVPI-QWWZWVQMSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 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
Agaricus bisporusFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Anas platyrhynchosFooDB
AnatidaeFooDB
Anethum graveolensLOTUS Database
Annona squamosaLOTUS Database
Anser anserFooDB
Arabidopsis thalianaLOTUS Database
Averrhoa carambolaKNApSAcK Database
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Cajanus cajanLOTUS Database
Capra aegagrus hircusFooDB
Carum carviFooDB
CervidaeFooDB
Cervus canadensisFooDB
Cnidium monnieriLOTUS Database
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Foeniculum vulgareLOTUS Database
Gallus gallusFooDB
Glehnia littoralisLOTUS Database
Homo sapiens (Urine)Animalia
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
Parmotrema cetratumLOTUS Database
PhasianidaeFooDB
Phasianus colchicusFooDB
Pleurotus ostreatusFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Pogostemon cablinLOTUS Database
Pycnandra acuminataLOTUS Database
Sebertia acuminataKNApSAcK Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Triticum aestivumKNApSAcK 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
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility1160 g/LALOGPS
logP-2.5ChemAxon
pKa (Strongest Acidic)13.04ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area80.92 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity26.48 m³·mol⁻¹ChemAxon
Polarizability11.66 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0004136
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB002261
KNApSAcK IDC00034313
Chemspider ID147828
KEGG Compound IDC16884
BioCyc IDCPD-12825
BiGG IDNot Available
Wikipedia LinkThreitol
METLIN IDNot Available
PubChem Compound169019
PDB IDNot Available
ChEBI ID48300
Good Scents IDrw1242041
References
General References
  1. Huck JH, Verhoeven NM, Struys EA, Salomons GS, Jakobs C, van der Knaap MS: Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy. Am J Hum Genet. 2004 Apr;74(4):745-51. Epub 2004 Feb 25. [PubMed:14988808 ]
  2. Wamelink MM, Smith DE, Jakobs C, Verhoeven NM: Analysis of polyols in urine by liquid chromatography-tandem mass spectrometry: a useful tool for recognition of inborn errors affecting polyol metabolism. J Inherit Metab Dis. 2005;28(6):951-63. [PubMed:16435188 ]
  3. Pitkanen E: The conversion of D-xylose into D-threitol in patients without liver disease and in patients with portal liver cirrhosis. Clin Chim Acta. 1977 Oct 1;80(1):49-54. [PubMed:908147 ]
  4. Jeffrey GA, Huang DB: The crystal structure of D-threitol at 119 K and 198 K. Carbohydr Res. 1992 Jan;223:11-8. doi: 10.1016/0008-6215(92)80002-i. [PubMed:1596913 ]
  5. Birkinshaw JH, Stickings CE, Tessier P: Biochemistry of the wood-rotting fungi: 5. The production of d-threitol (l-erythritol) by Armillaria mellea (Vahl) Quelet. Biochem J. 1948;42(3):329-32. [PubMed:16748290 ]