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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:53:41 UTC

Update Date

2023-02-21 17:23:03 UTC

HMDB ID

HMDB0033092

Secondary Accession Numbers

HMDB33092

Metabolite Identification

Common Name

3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid

Description

3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. Based on a literature review a small amount of articles have been published on 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0033092
     RDKit          3D
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid
 28 27  0  0  0  0  0  0  0  0999 V2000
    3.1891   -0.3283   -0.5924 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7240   -0.5898   -0.4747 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0369    0.1428    0.3542 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6970    1.1970    1.1440 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5542    0.9707    2.5226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4399   -0.0882    0.5243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0376    1.2220   -0.0328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4831    1.3224    0.0161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0959    1.5519    1.0832 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2265    1.1639   -1.1452 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8192   -1.2347   -0.3751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1995   -1.6759   -0.3368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0077   -1.3490    0.5433 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6541   -2.5176   -1.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6145   -1.0764   -1.2825 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7304   -0.4680    0.3627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3036    0.6438   -1.0663 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3406   -1.3840   -1.1014 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7979    1.2214    0.9814 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3382    2.2015    0.8527 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3380    0.4585    2.8736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7246   -0.2290    1.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6236    2.0660    0.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6327    1.3744   -1.0774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4607    2.0359   -1.6438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1643   -2.1355   -0.1418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5654   -0.9876   -1.4429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5295   -3.5082   -1.3524 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 14 28  1  0
M  END


  Mrv0541 02241209312D          

 14 13  0  0  0  0            999 V2000
   -1.4430   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062   -1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8553   -1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184   -2.1439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184    0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062    1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0306   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184    2.1439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184    1.4292    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8553   -0.7146    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184   -1.4292    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  4  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
 10 13  1  0  0  0  0
 10 14  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033092

> <DATABASE_NAME>
hmdb

> <SMILES>
C\C=C(/CO)C(CC(O)=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14O5/c1-2-6(5-10)7(3-8(11)12)4-9(13)14/h2,7,10H,3-5H2,1H3,(H,11,12)(H,13,14)/b6-2+

> <INCHI_KEY>
FUMUSIMACHNZQF-QHHAFSJGSA-N

> <FORMULA>
C9H14O5

> <MOLECULAR_WEIGHT>
202.2045

> <EXACT_MASS>
202.084123558

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
19.46576894043794

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(2Z)-1-hydroxybut-2-en-2-yl]pentanedioic acid

> <ALOGPS_LOGP>
0.07

> <JCHEM_LOGP>
-0.17708941766666672

> <ALOGPS_LOGS>
-1.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.7155394020362404

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.987878471650757

> <JCHEM_PKA_STRONGEST_BASIC>
-1.778809481325288

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
49.06190000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.62e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2Z)-1-hydroxybut-2-en-2-yl]pentanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0033092
     RDKit          3D
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid
 28 27  0  0  0  0  0  0  0  0999 V2000
    3.1891   -0.3283   -0.5924 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7240   -0.5898   -0.4747 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0369    0.1428    0.3542 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6970    1.1970    1.1440 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5542    0.9707    2.5226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4399   -0.0882    0.5243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0376    1.2220   -0.0328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4831    1.3224    0.0161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0959    1.5519    1.0832 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2265    1.1639   -1.1452 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8192   -1.2347   -0.3751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1995   -1.6759   -0.3368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0077   -1.3490    0.5433 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6541   -2.5176   -1.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6145   -1.0764   -1.2825 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7304   -0.4680    0.3627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3036    0.6438   -1.0663 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3406   -1.3840   -1.1014 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7979    1.2214    0.9814 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3382    2.2015    0.8527 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3380    0.4585    2.8736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7246   -0.2290    1.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6236    2.0660    0.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6327    1.3744   -1.0774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4607    2.0359   -1.6438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1643   -2.1355   -0.1418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5654   -0.9876   -1.4429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5295   -3.5082   -1.3524 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 14 28  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.694  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.154  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.385  -2.668   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.463  -2.668   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.385   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.154  -4.002   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.154   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.154   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.385   2.668   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.924  -1.334   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.154   4.002   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.154   2.668   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.463  -1.334   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.154  -2.668   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    3    5                                                  
CONECT    3    2    6                                                       
CONECT    4    1                                                            
CONECT    5    2    7    8                                                  
CONECT    6    3                                                            
CONECT    7    5    9                                                       
CONECT    8    5   10                                                       
CONECT    9    7   11   12                                                  
CONECT   10    8   13   14                                                  
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13   10                                                            
CONECT   14   10                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

COMPND    HMDB0033092
HETATM    1  C1  UNL     1       3.189  -0.328  -0.592  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.724  -0.590  -0.475  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.037   0.143   0.354  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.697   1.197   1.144  1.00  0.00           C  
HETATM    5  O1  UNL     1       1.554   0.971   2.523  1.00  0.00           O  
HETATM    6  C5  UNL     1      -0.440  -0.088   0.524  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.038   1.222  -0.033  1.00  0.00           C  
HETATM    8  C7  UNL     1      -2.483   1.322   0.016  1.00  0.00           C  
HETATM    9  O2  UNL     1      -3.096   1.552   1.083  1.00  0.00           O  
HETATM   10  O3  UNL     1      -3.226   1.164  -1.145  1.00  0.00           O  
HETATM   11  C8  UNL     1      -0.819  -1.235  -0.375  1.00  0.00           C  
HETATM   12  C9  UNL     1      -2.200  -1.676  -0.337  1.00  0.00           C  
HETATM   13  O4  UNL     1      -3.008  -1.349   0.543  1.00  0.00           O  
HETATM   14  O5  UNL     1      -2.654  -2.518  -1.348  1.00  0.00           O  
HETATM   15  H1  UNL     1       3.615  -1.076  -1.283  1.00  0.00           H  
HETATM   16  H2  UNL     1       3.730  -0.468   0.363  1.00  0.00           H  
HETATM   17  H3  UNL     1       3.304   0.644  -1.066  1.00  0.00           H  
HETATM   18  H4  UNL     1       1.341  -1.384  -1.101  1.00  0.00           H  
HETATM   19  H5  UNL     1       2.798   1.221   0.981  1.00  0.00           H  
HETATM   20  H6  UNL     1       1.338   2.201   0.853  1.00  0.00           H  
HETATM   21  H7  UNL     1       2.338   0.459   2.874  1.00  0.00           H  
HETATM   22  H8  UNL     1      -0.725  -0.229   1.561  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.624   2.066   0.593  1.00  0.00           H  
HETATM   24  H10 UNL     1      -0.633   1.374  -1.077  1.00  0.00           H  
HETATM   25  H11 UNL     1      -3.461   2.036  -1.644  1.00  0.00           H  
HETATM   26  H12 UNL     1      -0.164  -2.135  -0.142  1.00  0.00           H  
HETATM   27  H13 UNL     1      -0.565  -0.988  -1.443  1.00  0.00           H  
HETATM   28  H14 UNL     1      -2.530  -3.508  -1.352  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    3   18
CONECT    3    4    6
CONECT    4    5   19   20
CONECT    5   21
CONECT    6    7   11   22
CONECT    7    8   23   24
CONECT    8    9    9   10
CONECT   10   25
CONECT   11   12   26   27
CONECT   12   13   13   14
CONECT   14   28
END

HMDB0033092
     RDKit          3D
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid
 28 27  0  0  0  0  0  0  0  0999 V2000
    3.1891   -0.3283   -0.5924 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7240   -0.5898   -0.4747 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0369    0.1428    0.3542 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6970    1.1970    1.1440 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5542    0.9707    2.5226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4399   -0.0882    0.5243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0376    1.2220   -0.0328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4831    1.3224    0.0161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0959    1.5519    1.0832 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2265    1.1639   -1.1452 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8192   -1.2347   -0.3751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1995   -1.6759   -0.3368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0077   -1.3490    0.5433 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6541   -2.5176   -1.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6145   -1.0764   -1.2825 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7304   -0.4680    0.3627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3036    0.6438   -1.0663 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3406   -1.3840   -1.1014 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7979    1.2214    0.9814 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3382    2.2015    0.8527 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3380    0.4585    2.8736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7246   -0.2290    1.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6236    2.0660    0.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6327    1.3744   -1.0774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4607    2.0359   -1.6438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1643   -2.1355   -0.1418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5654   -0.9876   -1.4429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5295   -3.5082   -1.3524 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 14 28  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-(1-Hydroxymethyl-1-propenyl)pentanedioate	Generator
3-(1-Hydroxymethyl-1-propenyl)glutaric acid	HMDB
3-[(2Z)-1-Hydroxybut-2-en-2-yl]pentanedioate	Generator

Chemical Formula

C₉H₁₄O₅

Average Molecular Weight

202.2045

Monoisotopic Molecular Weight

202.084123558

IUPAC Name

3-[(2Z)-1-hydroxybut-2-en-2-yl]pentanedioic acid

Traditional Name

3-[(2Z)-1-hydroxybut-2-en-2-yl]pentanedioic acid

CAS Registry Number

Not Available

SMILES

C\C=C(/CO)C(CC(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C9H14O5/c1-2-6(5-10)7(3-8(11)12)4-9(13)14/h2,7,10H,3-5H2,1H3,(H,11,12)(H,13,14)/b6-2+

InChI Key

FUMUSIMACHNZQF-QHHAFSJGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Hydroxy fatty acid
Branched fatty acid
Unsaturated fatty acid
Dicarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Organelle

Adiposome (HMDB: HMDB0033092)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0033092)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033092)

Source

Endogenous

Endogenous (HMDB: HMDB0033092)

Plant

Plant (HMDB: HMDB0033092)

Animal

Animal (HMDB: HMDB0033092)

Exogenous

Food

Food (HMDB: HMDB0033092)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Fruit

Fruits (FooDB: FOOD00871)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Exogenous (HMDB: HMDB0033092)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0033092)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0033092)

Lipid metabolism pathway (HMDB: HMDB0033092)

Biochemical process

Lipid transport (HMDB: HMDB0033092)

Role

Biological role

Energy source (HMDB: HMDB0033092)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	7.62 g/L	ALOGPS
logP	0.07	ALOGPS
logP	-0.18	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	3.99	ChemAxon
pKa (Strongest Basic)	-1.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	49.06 m³·mol⁻¹	ChemAxon
Polarizability	19.47 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	148.122	31661259
DarkChem	[M-H]-	144.559	31661259
DeepCCS	[M+H]+	142.312	30932474
DeepCCS	[M-H]-	138.485	30932474
DeepCCS	[M-2H]-	176.058	30932474
DeepCCS	[M+Na]+	151.597	30932474
AllCCS	[M+H]+	146.8	32859911
AllCCS	[M+H-H2O]+	143.1	32859911
AllCCS	[M+NH4]+	150.2	32859911
AllCCS	[M+Na]+	151.2	32859911
AllCCS	[M-H]-	142.0	32859911
AllCCS	[M+Na-2H]-	143.1	32859911
AllCCS	[M+HCOO]-	144.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	2.83 minutes	32390414
Predicted by Siyang on May 30, 2022	9.4427 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.47 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	217.5 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1011.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	245.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	75.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	159.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	48.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	264.5 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	257.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	260.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	600.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	168.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	803.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	179.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	183.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	476.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	246.0 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	332.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid	C\C=C(/CO)C(CC(O)=O)CC(O)=O	3078.4	Standard polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid	C\C=C(/CO)C(CC(O)=O)CC(O)=O	1489.6	Standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid	C\C=C(/CO)C(CC(O)=O)CC(O)=O	1807.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,1TMS,isomer #1	C/C=C(\CO[Si](C)(C)C)C(CC(=O)O)CC(=O)O	1750.4	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,1TMS,isomer #2	C/C=C(\CO)C(CC(=O)O)CC(=O)O[Si](C)(C)C	1748.3	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,2TMS,isomer #1	C/C=C(\CO[Si](C)(C)C)C(CC(=O)O)CC(=O)O[Si](C)(C)C	1835.4	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,2TMS,isomer #2	C/C=C(\CO)C(CC(=O)O[Si](C)(C)C)CC(=O)O[Si](C)(C)C	1793.5	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,3TMS,isomer #1	C/C=C(\CO[Si](C)(C)C)C(CC(=O)O[Si](C)(C)C)CC(=O)O[Si](C)(C)C	1855.2	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,1TBDMS,isomer #1	C/C=C(\CO[Si](C)(C)C(C)(C)C)C(CC(=O)O)CC(=O)O	2024.0	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,1TBDMS,isomer #2	C/C=C(\CO)C(CC(=O)O)CC(=O)O[Si](C)(C)C(C)(C)C	2005.9	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,2TBDMS,isomer #1	C/C=C(\CO[Si](C)(C)C(C)(C)C)C(CC(=O)O)CC(=O)O[Si](C)(C)C(C)(C)C	2316.9	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,2TBDMS,isomer #2	C/C=C(\CO)C(CC(=O)O[Si](C)(C)C(C)(C)C)CC(=O)O[Si](C)(C)C(C)(C)C	2254.7	Semi standard non polar	33892256
3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid,3TBDMS,isomer #1	C/C=C(\CO[Si](C)(C)C(C)(C)C)C(CC(=O)O[Si](C)(C)C(C)(C)C)CC(=O)O[Si](C)(C)C(C)(C)C	2522.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-006x-5900000000-f6f9f5584cb91a47ee30	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid GC-MS (3 TMS) - 70eV, Positive	splash10-0fmr-9225200000-4a028dcd97f15c9d80a3	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 10V, Positive-QTOF	splash10-0f79-0920000000-ab97819dbc0fc1f1576f	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 20V, Positive-QTOF	splash10-000i-1900000000-b699603a875d80998134	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 40V, Positive-QTOF	splash10-000i-4900000000-ef9aeab1df4c7ffae94f	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 10V, Negative-QTOF	splash10-0udi-0980000000-ef2e42686520b6a98974	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 20V, Negative-QTOF	splash10-0zmi-1920000000-428086d47600a332f963	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 40V, Negative-QTOF	splash10-0r93-6900000000-b83e87b181e808f2adcf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 10V, Positive-QTOF	splash10-0553-1900000000-cefa232eb13cf5496b87	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 20V, Positive-QTOF	splash10-000i-7900000000-081d58f38c7de6352c73	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 40V, Positive-QTOF	splash10-059i-9100000000-ad4d1d40b475ae66766e	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 10V, Negative-QTOF	splash10-0ue9-0960000000-2f9ffebb4507422c12a2	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 20V, Negative-QTOF	splash10-0pei-3900000000-74caeb1d92fe884c5e6f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid 40V, Negative-QTOF	splash10-052f-9000000000-bf08ac47e02baad7695e	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB011087

KNApSAcK ID

Not Available

Chemspider ID

25936984

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101414422

PDB ID

Not Available

ChEBI ID

165379

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid (HMDB0033092)

MOL for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

3D MOL for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

3D SDF for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

3D-SDF for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

PDB for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

3D PDB for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

SMILES for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

INCHI for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

Structure for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

3D Structure for HMDB0033092 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra