NP-MRD: Showing NP-Card for 3-Hydroxysebacic acid (NP0000853)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2020-11-24 22:18:49 UTC

NP-MRD ID

NP0000853

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-Hydroxysebacic acid

Description

3-Hydroxysebacic acid is a normal urinary 3-hydroxydicarboxylic acid metabolite and can be elevated in patients with peroxisomal disorders such as Zellweger syndrome. Marked elevation of urinary 3- Hydroxysebacic acid has also been described in a malnourished infant with glycogen storage disease, mimicking long-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency (OMIM 300438 ), a defect in the beta-oxidation of fatty acids characterized by massive excretion of 3-hydroxydicarboxylic acids in the urine and accumulation of 3-hydroxy fatty acids in serum (PMID 12860034 , 14708889 , 8295400 ). 3-Hydroxysebacic acid is also found to be associated with medium-chain Acyl-CoA dehydrogenase deficiency, which is an inborn error of metabolism.

Structure

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

HMDB0000350
     RDKit          3D
3-Hydroxysebacic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    5.0130    1.0438   -1.2693 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9583    0.4051   -1.4987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9162    1.0409   -2.1373 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8128   -1.0010   -1.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5182   -1.0738    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404   -0.3381    0.7025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0493   -0.9154   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1580   -0.0949    0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4210   -0.5819   -0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5455    0.3295    0.2188 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3045    1.6501   -0.1074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8797   -0.0846   -0.3466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9064    0.8245    0.1746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1078    0.6402   -0.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6532    1.8746    1.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6093    1.9654   -1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0115   -1.4801   -1.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7861   -1.5379   -1.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5410   -2.0937    0.7584 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3383   -0.5090    0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3688    0.7046    0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0282   -0.3653    1.7719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133   -1.9938    0.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1617   -0.8255   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520    0.9491    0.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2976   -0.1406    1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6524   -1.6124    0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -0.5180   -1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6237    0.2539    1.3294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6585    1.7920   -1.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334   -0.0052   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1004   -1.1475   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8081    2.8448    0.7924 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
M  END


  Mrv1652303062020102D          

 15 14  0  0  0  0            999 V2000
   16.6711  -14.0637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5277  -15.3012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.3871  -14.8887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2421  -14.0637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.6725  -16.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.1002  -14.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8146  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3856  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.5292  -14.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6711  -14.8887    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   20.2436  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9566  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.9580  -14.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2421  -14.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.6725  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 10  1  1  6  0  0  0
  2 14  1  0  0  0  0
  3 15  1  0  0  0  0
  4 14  2  0  0  0  0
  5 15  2  0  0  0  0
  6  7  1  0  0  0  0
  6  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
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000853

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H](CCCCCCC(O)=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O5/c11-8(7-10(14)15)5-3-1-2-4-6-9(12)13/h8,11H,1-7H2,(H,12,13)(H,14,15)/t8-/m1/s1

> <INCHI_KEY>
OQYZCCKCJQWHIE-MRVPVSSYSA-N

> <FORMULA>
C10H18O5

> <MOLECULAR_WEIGHT>
218.249

> <EXACT_MASS>
218.11542368

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.362731405302434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-3-hydroxydecanedioic acid

> <ALOGPS_LOGP>
0.63

> <JCHEM_LOGP>
1.0381179556666666

> <ALOGPS_LOGS>
-1.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.052863606302775

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.450063494495128

> <JCHEM_PKA_STRONGEST_BASIC>
-2.798587427000225

> <JCHEM_POLAR_SURFACE_AREA>
94.82999999999998

> <JCHEM_REFRACTIVITY>
52.658500000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.38e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-hydroxydecanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000350
     RDKit          3D
3-Hydroxysebacic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    5.0130    1.0438   -1.2693 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9583    0.4051   -1.4987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9162    1.0409   -2.1373 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8128   -1.0010   -1.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5182   -1.0738    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404   -0.3381    0.7025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0493   -0.9154   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1580   -0.0949    0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4210   -0.5819   -0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5455    0.3295    0.2188 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3045    1.6501   -0.1074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8797   -0.0846   -0.3466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9064    0.8245    0.1746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1078    0.6402   -0.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6532    1.8746    1.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6093    1.9654   -1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0115   -1.4801   -1.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7861   -1.5379   -1.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5410   -2.0937    0.7584 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3383   -0.5090    0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3688    0.7046    0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0282   -0.3653    1.7719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133   -1.9938    0.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1617   -0.8255   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520    0.9491    0.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2976   -0.1406    1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6524   -1.6124    0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -0.5180   -1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6237    0.2539    1.3294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6585    1.7920   -1.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334   -0.0052   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1004   -1.1475   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8081    2.8448    0.7924 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
M  END

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  O   UNK     0      31.119 -26.252   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      27.118 -28.562   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      41.789 -27.792   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      28.452 -26.252   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      40.455 -30.102   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      33.787 -27.792   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      35.121 -28.562   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      32.453 -28.562   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      36.455 -27.792   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.119 -27.792   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      37.788 -28.562   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      29.786 -28.562   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      39.122 -27.792   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      28.452 -27.792   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      40.455 -28.562   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4   14                                                            
CONECT    5   15                                                            
CONECT    6    7    8                                                       
CONECT    7    6    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    1    8   12                                                  
CONECT   11    9   13                                                       
CONECT   12   10   14                                                       
CONECT   13   11   15                                                       
CONECT   14    2    4   12                                                  
CONECT   15    3    5   13                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

COMPND    HMDB0000350
HETATM    1  O1  UNL     1       5.013   1.044  -1.269  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.958   0.405  -1.499  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.916   1.041  -2.137  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.813  -1.001  -1.102  1.00  0.00           C  
HETATM    5  C3  UNL     1       3.518  -1.074   0.374  1.00  0.00           C  
HETATM    6  C4  UNL     1       2.240  -0.338   0.702  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.049  -0.915  -0.028  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.158  -0.095   0.386  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.421  -0.582  -0.287  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.546   0.329   0.219  1.00  0.00           C  
HETATM   11  O3  UNL     1      -2.305   1.650  -0.107  1.00  0.00           O  
HETATM   12  C9  UNL     1      -3.880  -0.085  -0.347  1.00  0.00           C  
HETATM   13  C10 UNL     1      -4.906   0.825   0.175  1.00  0.00           C  
HETATM   14  O4  UNL     1      -6.108   0.640  -0.187  1.00  0.00           O  
HETATM   15  O5  UNL     1      -4.653   1.875   1.038  1.00  0.00           O  
HETATM   16  H1  UNL     1       2.609   1.965  -1.854  1.00  0.00           H  
HETATM   17  H2  UNL     1       3.011  -1.480  -1.689  1.00  0.00           H  
HETATM   18  H3  UNL     1       4.786  -1.538  -1.273  1.00  0.00           H  
HETATM   19  H4  UNL     1       3.541  -2.094   0.758  1.00  0.00           H  
HETATM   20  H5  UNL     1       4.338  -0.509   0.894  1.00  0.00           H  
HETATM   21  H6  UNL     1       2.369   0.705   0.344  1.00  0.00           H  
HETATM   22  H7  UNL     1       2.028  -0.365   1.772  1.00  0.00           H  
HETATM   23  H8  UNL     1       0.913  -1.994   0.201  1.00  0.00           H  
HETATM   24  H9  UNL     1       1.162  -0.825  -1.136  1.00  0.00           H  
HETATM   25  H10 UNL     1       0.052   0.949   0.124  1.00  0.00           H  
HETATM   26  H11 UNL     1      -0.298  -0.141   1.483  1.00  0.00           H  
HETATM   27  H12 UNL     1      -1.652  -1.612   0.053  1.00  0.00           H  
HETATM   28  H13 UNL     1      -1.368  -0.518  -1.374  1.00  0.00           H  
HETATM   29  H14 UNL     1      -2.624   0.254   1.329  1.00  0.00           H  
HETATM   30  H15 UNL     1      -2.658   1.792  -1.026  1.00  0.00           H  
HETATM   31  H16 UNL     1      -3.833  -0.005  -1.451  1.00  0.00           H  
HETATM   32  H17 UNL     1      -4.100  -1.147  -0.088  1.00  0.00           H  
HETATM   33  H18 UNL     1      -4.808   2.845   0.792  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   16
CONECT    4    5   17   18
CONECT    5    6   19   20
CONECT    6    7   21   22
CONECT    7    8   23   24
CONECT    8    9   25   26
CONECT    9   10   27   28
CONECT   10   11   12   29
CONECT   11   30
CONECT   12   13   31   32
CONECT   13   14   14   15
CONECT   15   33
END

HMDB0000350
     RDKit          3D
3-Hydroxysebacic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    5.0130    1.0438   -1.2693 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9583    0.4051   -1.4987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9162    1.0409   -2.1373 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8128   -1.0010   -1.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5182   -1.0738    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404   -0.3381    0.7025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0493   -0.9154   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1580   -0.0949    0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4210   -0.5819   -0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5455    0.3295    0.2188 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3045    1.6501   -0.1074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8797   -0.0846   -0.3466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9064    0.8245    0.1746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1078    0.6402   -0.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6532    1.8746    1.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6093    1.9654   -1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0115   -1.4801   -1.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7861   -1.5379   -1.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5410   -2.0937    0.7584 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3383   -0.5090    0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3688    0.7046    0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0282   -0.3653    1.7719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133   -1.9938    0.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1617   -0.8255   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520    0.9491    0.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2976   -0.1406    1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6524   -1.6124    0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -0.5180   -1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6237    0.2539    1.3294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6585    1.7920   -1.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334   -0.0052   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1004   -1.1475   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8081    2.8448    0.7924 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
M  END

View in JSmol

Synonyms

Value	Source
3-Hydroxysebacate	Generator
(R)-3-Hydroxydecanedioic acid	HMDB
(R)-3-Hydroxysebacic acid	HMDB
3-Hydroxydecanedioic acid	HMDB
3-Hydroxy-decanedioic acid	HMDB
3-Hydroxy-sebacic acid	HMDB
3-Hydroxy-decanedioate	HMDB
3-Hydroxy-sebacate	HMDB
3-Hydroxydecanedioate	HMDB
3-Hydroxysebacic acid	HMDB
(3R)-3-Hydroxydecanedioate	Generator

Chemical Formula

C₁₀H₁₈O₅

Average Mass

218.2469 Da

Monoisotopic Mass

218.11542 Da

IUPAC Name

(3R)-3-hydroxydecanedioic acid

Traditional Name

(3R)-3-hydroxydecanedioic acid

CAS Registry Number

73141-46-5

SMILES

OC(CCCCCCC(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C10H18O5/c11-8(7-10(14)15)5-3-1-2-4-6-9(12)13/h8,11H,1-7H2,(H,12,13)(H,14,15)

InChI Key

OQYZCCKCJQWHIE-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, simulated)	v.dorna83@yahoo.com	Not Available	Not Available	2021-08-10	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Species Where Detected

Species Name	Source	Reference
Homo sapiens (Urine)	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Medium-chain fatty acid
Hydroxy fatty acid
Beta-hydroxy acid
Fatty acyl
Fatty acid
Dicarboxylic acid or derivatives
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Physical Properties

State

Solid

Experimental 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

Predicted Properties

Property	Value	Source
Water Solubility	3.38 g/L	ALOGPS
logP	0.63	ALOGPS
logP	1.04	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	4.45	ChemAxon
pKa (Strongest Basic)	-2.8	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	9	ChemAxon
Refractivity	52.66 m³·mol⁻¹	ChemAxon
Polarizability	23.36 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

External Links

HMDB ID

HMDB0000350

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021973

KNApSAcK ID

C00052146

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

124350389

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Muth A, Jung J, Bilke S, Scharrer A, Mosandl A, Sewell AC, Bohles H: Simultaneous enantioselective analysis of chiral urinary metabolites in patients with Zellweger syndrome. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 25;792(2):269-77. [PubMed:12860034 ]
Muth A, Mosandl A, Wanders RJ, Nowaczyk MJ, Baric I, Bohles H, Sewell AC: Stereoselective analysis of 2-hydroxysebacic acid in urine of patients with Zellweger syndrome and of premature infants fed with medium-chain triglycerides. J Inherit Metab Dis. 2003;26(6):583-92. [PubMed:14605504 ]
Bergoffen J, Kaplan P, Hale DE, Bennett MJ, Berry GT: Marked elevation of urinary 3-hydroxydecanedioic acid in a malnourished infant with glycogen storage disease, mimicking long-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency. J Inherit Metab Dis. 1993;16(5):851-6. [PubMed:8295400 ]
Peron G, Dall'Acqua S, Sut S: Supplementation with resveratrol as Polygonum cuspidatum Sieb. et Zucc. extract induces changes in the excretion of urinary markers associated to aging in rats. Fitoterapia. 2018 Sep;129:154-161. doi: 10.1016/j.fitote.2018.06.022. Epub 2018 Jun 27. [PubMed:29959053 ]

Showing NP-Card for 3-Hydroxysebacic acid (NP0000853)

MOL for NP0000853 (3-Hydroxysebacic acid)

3D MOL for NP0000853 (3-Hydroxysebacic acid)

3D SDF for NP0000853 (3-Hydroxysebacic acid)

3D-SDF for NP0000853 (3-Hydroxysebacic acid)

PDB for NP0000853 (3-Hydroxysebacic acid)

3D PDB for NP0000853 (3-Hydroxysebacic acid)

SMILES for NP0000853 (3-Hydroxysebacic acid)

INCHI for NP0000853 (3-Hydroxysebacic acid)

Structure for NP0000853 (3-Hydroxysebacic acid)

3D Structure for NP0000853 (3-Hydroxysebacic acid)