Showing metabocard for Erythrose (MMDBc0000593)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:50:41 UTC
Update Date2024-04-30 19:33:10 UTC
Metabolite IDMMDBc0000593
Metabolite Identification
Common NameErythrose
DescriptionErythrose is a tetrose saccharide with the chemical formula C4H8O4. It has one aldehyde group, and is thus part of the aldose family. The natural isomer is D-erythrose. It is a member of the class of compounds known as pentoses. Pentoses are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Erythrose is very soluble (in water). Erythrose can be found in blood, as well as in human cartilage tissue. Within the cell, erythrose is primarily located in the cytoplasm (predicted from logP). Erythrose exists in all living organisms, ranging from bacteria to humans. Erythrose is found to be associated with schizophrenia. Erythrose was first isolated in 1849 from rhubarb by the French pharmacist Louis Feux Joseph Garot (1798-1869) and was named as such because of its red hue in the presence of alkali metals.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fd0cd2e5c48>


  Mrv1652305271900112D          

 11 11  0  0  1  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298   -0.8903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  2  5  1  6  0  0  0
  3  6  1  6  0  0  0
  7  4  1  0  0  0  0
  8  1  1  0  0  0  0
  8  4  1  0  0  0  0
  2  9  1  1  0  0  0
  3 10  1  1  0  0  0
 11  4  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fd0cd2e5c48>

HMDB0002649
     RDKit          3D
Erythrose
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.3064   -0.3141    0.7310 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1502   -0.4410    0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127   -1.4532    0.4255 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9913   -1.0733    0.1794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9468    0.2058   -0.5914 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0477    0.9928   -0.4901 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3047    0.8398    0.0374 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0551    1.2625    1.3241 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0698   -0.6328    0.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651   -0.6188   -1.0726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5496   -1.8471   -0.3800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5578   -0.9323    1.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6737    0.0073   -1.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0046    1.6662   -1.2400 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7006    1.6108   -0.6167 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5070    0.7274    2.0247 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  6
  6 14  1  0
  7 15  1  6
  8 16  1  0
M  END
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3D SDF for #<Metabolite:0x00007fd0cd2e5c48>


  Mrv1652305271900112D          

 11 11  0  0  1  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298   -0.8903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  2  5  1  6  0  0  0
  3  6  1  6  0  0  0
  7  4  1  0  0  0  0
  8  1  1  0  0  0  0
  8  4  1  0  0  0  0
  2  9  1  1  0  0  0
  3 10  1  1  0  0  0
 11  4  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000593

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O)COC([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O4/c5-2-1-8-4(7)3(2)6/h2-7H,1H2/t2-,3-,4?/m1/s1

> <INCHI_KEY>
FMAORJIQYMIRHF-HERZVMAMSA-N

> <FORMULA>
C4H8O4

> <MOLECULAR_WEIGHT>
120.1039

> <EXACT_MASS>
120.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
10.733662836452542

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R)-oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.30

> <JCHEM_LOGP>
-1.671869334

> <ALOGPS_LOGS>
1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.052554670413375

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.32050975209086

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5572951827239905

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
23.998399999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.43e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-erythro-tetrose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fd0cd2e5c48>

HMDB0002649
     RDKit          3D
Erythrose
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.3064   -0.3141    0.7310 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1502   -0.4410    0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127   -1.4532    0.4255 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9913   -1.0733    0.1794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9468    0.2058   -0.5914 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0477    0.9928   -0.4901 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3047    0.8398    0.0374 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0551    1.2625    1.3241 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0698   -0.6328    0.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651   -0.6188   -1.0726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5496   -1.8471   -0.3800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5578   -0.9323    1.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6737    0.0073   -1.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0046    1.6662   -1.2400 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7006    1.6108   -0.6167 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5070    0.7274    2.0247 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  6
  6 14  1  0
  7 15  1  6
  8 16  1  0
M  END
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PDB for #<Metabolite:0x00007fd0cd2e5c48>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM    9  H   UNK     0      -0.312   2.779   0.000  0.00  0.00           H+0
HETATM   10  H   UNK     0      -1.275   0.086   0.000  0.00  0.00           H+0
HETATM   11  H   UNK     0       0.989  -1.662   0.000  0.00  0.00           H+0
CONECT    1    2    8                                                       
CONECT    2    1    3    5    9                                             
CONECT    3    2    4    6   10                                             
CONECT    4    3    7    8   11                                             
CONECT    5    2                                                            
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    1    4                                                       
CONECT    9    2                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for #<Metabolite:0x00007fd0cd2e5c48>

COMPND    HMDB0002649
HETATM    1  O1  UNL     1       2.306  -0.314   0.731  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.150  -0.441   0.020  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.313  -1.453   0.425  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.991  -1.073   0.179  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.947   0.206  -0.591  1.00  0.00           C  
HETATM    6  O3  UNL     1      -2.048   0.993  -0.490  1.00  0.00           O  
HETATM    7  C4  UNL     1       0.305   0.840   0.037  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.055   1.262   1.324  1.00  0.00           O  
HETATM    9  H1  UNL     1       3.070  -0.633   0.155  1.00  0.00           H  
HETATM   10  H2  UNL     1       1.365  -0.619  -1.073  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.550  -1.847  -0.380  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.558  -0.932   1.138  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.674   0.007  -1.644  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.005   1.666  -1.240  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.701   1.611  -0.617  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.507   0.727   2.025  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3    7   10
CONECT    3    4
CONECT    4    5   11   12
CONECT    5    6    7   13
CONECT    6   14
CONECT    7    8   15
CONECT    8   16
END
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SMILES for #<Metabolite:0x00007fd0cd2e5c48>

[H][C@@]1(O)COC([H])(O)[C@]1([H])O
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INCHI for #<Metabolite:0x00007fd0cd2e5c48>

InChI=1S/C4H8O4/c5-2-1-8-4(7)3(2)6/h2-7H,1H2/t2-,3-,4?/m1/s1
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Synonyms
ValueSource
(R*,r*)-2,3,4-trihydroxybutanalHMDB
D-erythro-TetroseHMDB
D-ErythroseHMDB
L-threo-AldoseHMDB
L-ThreoseHMDB
LTrHMDB
ThreoseHMDB
Molecular FormulaC4H8O4
Average Mass120.1039
Monoisotopic Mass120.042258744
IUPAC Name(3R,4R)-oxolane-2,3,4-triol
Traditional NameD-erythro-tetrose
CAS Registry NumberNot Available
SMILES
[H][C@@]1(O)COC([H])(O)[C@]1([H])O
InChI Identifier
InChI=1S/C4H8O4/c5-2-1-8-4(7)3(2)6/h2-7H,1H2/t2-,3-,4?/m1/s1
InChI KeyFMAORJIQYMIRHF-HERZVMAMSA-N