Showing metabocard for D-threitol (MMDBc0054440)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:12:27 UTC
Update Date2024-04-30 20:53:08 UTC
Metabolite IDMMDBc0054440
Metabolite 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fa4b8fa0550>


  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
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3D MOL for #<Metabolite:0x00007fa4b8fa0550>

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
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3D SDF for #<Metabolite:0x00007fa4b8fa0550>


  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>
MMDBc0054440

> <DATABASE_NAME>
MIME

> <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

$$$$
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3D-SDF for #<Metabolite:0x00007fa4b8fa0550>

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
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PDB for #<Metabolite:0x00007fa4b8fa0550>

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 #<Metabolite:0x00007fa4b8fa0550>

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
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SMILES for #<Metabolite:0x00007fa4b8fa0550>

OC[C@@H](O)[C@H](O)CO
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INCHI for #<Metabolite:0x00007fa4b8fa0550>

InChI=1S/C4H10O4/c5-1-3(7)4(8)2-6/h3-8H,1-2H2/t3-,4-/m1/s1
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Synonyms
ValueSource
D-Threo-tetritolChEBI
(-)-ThreitolHMDB
(R*,r*)-1,2,3,4-butanetetrolHMDB
ThreitHMDB
ThreitolHMDB, MeSH
Threitol, ((r*,r*)-(+-))-isomerMeSH, HMDB
Threitol, (R-(r*,r*))-isomerMeSH, HMDB
1,2,3,4-TetrahydroxybutaneHMDB
Molecular FormulaC4H10O4
Average Mass122.1198
Monoisotopic Mass122.057908808
IUPAC Name(2R,3R)-butane-1,2,3,4-tetrol
Traditional Name(-)-threitol
CAS Registry NumberNot Available
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