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Showing metabocard for Nonate (HMDB0011717)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2009-02-24 15:43:08 UTC
Update Date2023-02-21 17:17:34 UTC
HMDB IDHMDB0011717
Secondary Accession Numbers
  • HMDB11717
Metabolite Identification
Common NameNonate
DescriptionNonic acid or the anion, nonate, is a derivative of succinic acid, which is a dicarboxylic acid. The anion, succinate, is a component of the citric acid cycle capable of donating electrons to the electron transfer chain. Succinate dehydrogenase (SDH) plays an important role in the mitochondria, being both part of the respiratory chain and the Krebs cycle. SDH with a covalently attached FAD prosthetic group, binds enzyme substrates (succinate and fumarate) and physiological regulators (oxaloacetate and ATP). Oxidizing succinate links SDH to the fast-cycling Krebs cycle portion where it participates in the breakdown of acetyl-CoA throughout the whole Krebs cycle. The succinate can readily be imported into the mitochondrial matrix by the n-butylmalonate- (or phenylsuccinate-) sensitive dicarboxylate carrier in exchange with inorganic phosphate or another organic acid, e. g. malate. (PMID 16143825 ) Mutations in the four genes encoding the subunits of the mitochondrial respiratory chain succinate dehydrogenase are associated with a wide spectrum of clinical presentations (i.e.: Huntington's disease. (PMID 11803021 ).
Structure
Data?1676999854
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011717 (Nonate)


  Mrv0541 02241201522D          

 13 12  0  0  1  0            999 V2000
    3.3694   -2.3442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9418   -3.5817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2274   -3.9942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5129   -3.5817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7984   -3.9942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0839   -3.5817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0839   -5.2317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6549   -5.2317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9405   -2.3442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6549   -2.7567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6549   -3.5817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3694   -3.9942    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3694   -4.8192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
  9 10  2  0  0  0  0
  8 13  2  0  0  0  0
  7 13  1  0  0  0  0
 12  6  1  6  0  0  0
  5  6  1  0  0  0  0
  4  5  1  0  0  0  0
  3  4  1  0  0  0  0
  2  3  1  0  0  0  0
  1 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0011717 (Nonate)

HMDB0011717
     RDKit          3D
Nonate
 29 28  0  0  0  0  0  0  0  0999 V2000
   -2.5864    1.4194   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6764    0.1178   -0.8338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2088   -0.9962    0.0382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7909   -0.8378    0.5212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1239   -0.7871   -0.6464 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5721   -0.6410   -0.3041 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9292    0.5734    0.4590 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6051    1.8396   -0.2444 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0871    1.9135   -1.3697 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9242    3.0203    0.4495 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0879   -1.8674    0.3490 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3265   -2.8331    0.5261 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4050   -1.9571    0.7659 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9600    1.2001    0.9697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5397    1.7386    0.0179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2587    2.1954   -0.4657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7639   -0.0253   -1.0686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1621    0.1945   -1.7909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9221   -1.0917    0.9105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3417   -1.9766   -0.5014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7074    0.1319    1.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5961   -1.7010    1.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2292   -0.0078   -1.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0038   -1.7568   -1.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1211   -0.5792   -1.2906 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4729    0.6454    1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0330    0.5977    0.6334 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8762    3.1724    0.7631 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1756   -1.7017    0.1731 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
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  2  0
 11 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  6
  7 26  1  0
  7 27  1  0
 10 28  1  0
 13 29  1  0
M  END
Download

3D SDF for HMDB0011717 (Nonate)


  Mrv0541 02241201522D          

 13 12  0  0  1  0            999 V2000
    3.3694   -2.3442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9418   -3.5817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2274   -3.9942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5129   -3.5817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7984   -3.9942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0839   -3.5817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0839   -5.2317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6549   -5.2317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9405   -2.3442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6549   -2.7567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6549   -3.5817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3694   -3.9942    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3694   -4.8192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
  9 10  2  0  0  0  0
  8 13  2  0  0  0  0
  7 13  1  0  0  0  0
 12  6  1  6  0  0  0
  5  6  1  0  0  0  0
  4  5  1  0  0  0  0
  3  4  1  0  0  0  0
  2  3  1  0  0  0  0
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011717

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H16O4/c1-2-3-4-5-7(9(12)13)6-8(10)11/h7H,2-6H2,1H3,(H,10,11)(H,12,13)/t7-/m0/s1

> <INCHI_KEY>
FNZSVEHJZREFPF-ZETCQYMHSA-N

> <FORMULA>
C9H16O4

> <MOLECULAR_WEIGHT>
188.2209

> <EXACT_MASS>
188.104859

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
19.973999345935646

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-2-pentylbutanedioic acid

> <ALOGPS_LOGP>
1.27

> <JCHEM_LOGP>
1.922777971

> <ALOGPS_LOGS>
-1.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.999371348781824

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.465192225919394

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
46.5155

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.86e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-pentylbutanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0011717 (Nonate)

HMDB0011717
     RDKit          3D
Nonate
 29 28  0  0  0  0  0  0  0  0999 V2000
   -2.5864    1.4194   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6764    0.1178   -0.8338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2088   -0.9962    0.0382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7909   -0.8378    0.5212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1239   -0.7871   -0.6464 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5721   -0.6410   -0.3041 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9292    0.5734    0.4590 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6051    1.8396   -0.2444 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0871    1.9135   -1.3697 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9242    3.0203    0.4495 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0879   -1.8674    0.3490 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3265   -2.8331    0.5261 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4050   -1.9571    0.7659 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9600    1.2001    0.9697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5397    1.7386    0.0179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2587    2.1954   -0.4657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7639   -0.0253   -1.0686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1621    0.1945   -1.7909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9221   -1.0917    0.9105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3417   -1.9766   -0.5014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7074    0.1319    1.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5961   -1.7010    1.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2292   -0.0078   -1.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0038   -1.7568   -1.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1211   -0.5792   -1.2906 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4729    0.6454    1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0330    0.5977    0.6334 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8762    3.1724    0.7631 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1756   -1.7017    0.1731 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
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  2  0
 11 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  6
  7 26  1  0
  7 27  1  0
 10 28  1  0
 13 29  1  0
M  END
Download

PDB for HMDB0011717 (Nonate)

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  O   UNK     0       6.290  -4.376   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      12.958  -6.686   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.624  -7.456   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.291  -6.686   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.957  -7.456   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.623  -6.686   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.623  -9.766   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.956  -9.766   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       3.622  -4.376   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.956  -5.146   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.956  -6.686   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.290  -7.456   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.290  -8.996   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2    3                                                            
CONECT    3    4    2                                                       
CONECT    4    5    3                                                       
CONECT    5    6    4                                                       
CONECT    6   12    5                                                       
CONECT    7   13                                                            
CONECT    8   13                                                            
CONECT    9   10                                                            
CONECT   10   11    9    1                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13    6                                                  
CONECT   13   12    8    7                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0011717 (Nonate)

COMPND    HMDB0011717
HETATM    1  C1  UNL     1      -2.586   1.419  -0.052  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.676   0.118  -0.834  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.209  -0.996   0.038  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.791  -0.838   0.521  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.124  -0.787  -0.646  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.572  -0.641  -0.304  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.929   0.573   0.459  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.605   1.840  -0.244  1.00  0.00           C  
HETATM    9  O1  UNL     1       1.087   1.914  -1.370  1.00  0.00           O  
HETATM   10  O2  UNL     1       1.924   3.020   0.449  1.00  0.00           O  
HETATM   11  C9  UNL     1       2.088  -1.867   0.349  1.00  0.00           C  
HETATM   12  O3  UNL     1       1.326  -2.833   0.526  1.00  0.00           O  
HETATM   13  O4  UNL     1       3.405  -1.957   0.766  1.00  0.00           O  
HETATM   14  H1  UNL     1      -2.960   1.200   0.970  1.00  0.00           H  
HETATM   15  H2  UNL     1      -1.540   1.739   0.018  1.00  0.00           H  
HETATM   16  H3  UNL     1      -3.259   2.195  -0.466  1.00  0.00           H  
HETATM   17  H4  UNL     1      -3.764  -0.025  -1.069  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.162   0.194  -1.791  1.00  0.00           H  
HETATM   19  H6  UNL     1      -2.922  -1.092   0.911  1.00  0.00           H  
HETATM   20  H7  UNL     1      -2.342  -1.977  -0.501  1.00  0.00           H  
HETATM   21  H8  UNL     1      -0.707   0.132   1.061  1.00  0.00           H  
HETATM   22  H9  UNL     1      -0.596  -1.701   1.196  1.00  0.00           H  
HETATM   23  H10 UNL     1      -0.229  -0.008  -1.351  1.00  0.00           H  
HETATM   24  H11 UNL     1       0.004  -1.757  -1.208  1.00  0.00           H  
HETATM   25  H12 UNL     1       2.121  -0.579  -1.291  1.00  0.00           H  
HETATM   26  H13 UNL     1       1.473   0.645   1.462  1.00  0.00           H  
HETATM   27  H14 UNL     1       3.033   0.598   0.633  1.00  0.00           H  
HETATM   28  H15 UNL     1       2.876   3.172   0.763  1.00  0.00           H  
HETATM   29  H16 UNL     1       4.176  -1.702   0.173  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3   17   18
CONECT    3    4   19   20
CONECT    4    5   21   22
CONECT    5    6   23   24
CONECT    6    7   11   25
CONECT    7    8   26   27
CONECT    8    9    9   10
CONECT   10   28
CONECT   11   12   12   13
CONECT   13   29
END
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SMILES for HMDB0011717 (Nonate)

CCCCC[C@@H](CC(O)=O)C(O)=O
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INCHI for HMDB0011717 (Nonate)

InChI=1S/C9H16O4/c1-2-3-4-5-7(9(12)13)6-8(10)11/h7H,2-6H2,1H3,(H,10,11)(H,12,13)/t7-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
NONic acidGenerator
(2R) - 2- PentylbutanedioateHMDB
(2R) - 2- Pentylbutanedioic acidHMDB
(2R) - 2- Pentylsuccinic acidHMDB
2- Pentylsuccinic acidHMDB
NONic acid EthanedisulfonateHMDB
(2S)-2-PentylbutanedioateGenerator, HMDB
Chemical FormulaC9H16O4
Average Molecular Weight188.2209
Monoisotopic Molecular Weight188.104859
IUPAC Name(2S)-2-pentylbutanedioic acid
Traditional Name(2S)-2-pentylbutanedioic acid
CAS Registry NumberNot Available
SMILES
CCCCC[C@@H](CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C9H16O4/c1-2-3-4-5-7(9(12)13)6-8(10)11/h7H,2-6H2,1H3,(H,10,11)(H,12,13)/t7-/m0/s1
InChI KeyFNZSVEHJZREFPF-ZETCQYMHSA-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Methyl-branched fatty acid
  • Branched fatty acid
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility3.86 g/LALOGPS
logP1.27ALOGPS
logP1.92ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)4.47ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity46.52 m³·mol⁻¹ChemAxon
Polarizability19.97 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+145.3931661259
DarkChem[M-H]-144.28531661259
DeepCCS[M+H]+143.64130932474
DeepCCS[M-H]-139.81430932474
DeepCCS[M-2H]-176.93230932474
DeepCCS[M+Na]+152.5230932474
AllCCS[M+H]+145.332859911
AllCCS[M+H-H2O]+141.532859911
AllCCS[M+NH4]+148.832859911
AllCCS[M+Na]+149.832859911
AllCCS[M-H]-143.332859911
AllCCS[M+Na-2H]-144.732859911
AllCCS[M+HCOO]-146.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.4.55 minutes32390414
Predicted by Siyang on May 30, 202211.1405 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.18 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid63.7 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1668.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid297.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid126.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid185.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid213.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid442.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid457.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)87.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid890.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid373.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1193.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid277.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid340.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate386.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA210.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water172.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
NonateCCCCC[C@@H](CC(O)=O)C(O)=O2472.5Standard polar33892256
NonateCCCCC[C@@H](CC(O)=O)C(O)=O1346.4Standard non polar33892256
NonateCCCCC[C@@H](CC(O)=O)C(O)=O1572.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Nonate,1TMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C)C(=O)O1571.2Semi standard non polar33892256
Nonate,1TMS,isomer #2CCCCC[C@@H](CC(=O)O)C(=O)O[Si](C)(C)C1527.7Semi standard non polar33892256
Nonate,2TMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1643.1Semi standard non polar33892256
Nonate,1TBDMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O1805.7Semi standard non polar33892256
Nonate,1TBDMS,isomer #2CCCCC[C@@H](CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C1760.6Semi standard non polar33892256
Nonate,2TBDMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2105.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Nonate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9500000000-38d1c2542c5109e116bf2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nonate GC-MS (2 TMS) - 70eV, Positivesplash10-00rf-9051000000-67ad3f607bb0d0d8c5062017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nonate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 10V, Positive-QTOFsplash10-00di-0900000000-f9d5425ef98bcbccbe4f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 20V, Positive-QTOFsplash10-00fu-5900000000-0096a6065c03ecab28fb2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 40V, Positive-QTOFsplash10-052e-9100000000-880e6119878c363e5c172017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 10V, Negative-QTOFsplash10-000l-0900000000-67d40c109b682dea3f482017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 20V, Negative-QTOFsplash10-00ko-1900000000-6c62d33822e53e2d220e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 40V, Negative-QTOFsplash10-0a4l-9100000000-5d00db6240f4db0ae3012017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 10V, Positive-QTOFsplash10-007d-5900000000-80d0f819a79928c38c752021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 20V, Positive-QTOFsplash10-00lu-9400000000-2ceb2add929c737793ff2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 40V, Positive-QTOFsplash10-05g0-9000000000-004722dc9eff5a2d96802021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 10V, Negative-QTOFsplash10-014i-0900000000-cba41d731216dc0d13542021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 20V, Negative-QTOFsplash10-0006-4900000000-98ea4b0f0f9da5458c1e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nonate 40V, Negative-QTOFsplash10-0006-9100000000-0e1f126dd8b4b5da89d82021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.5 (0.0-1.0) uMAdult (>18 years old)Both
Prostate Cancer		 details
Associated Disorders and Diseases
Disease References
Prostate cancer
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028402
KNApSAcK IDC00022257
Chemspider ID13183696
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound16058309
PDB IDNot Available
ChEBI ID88404
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Briere JJ, Favier J, El Ghouzzi V, Djouadi F, Benit P, Gimenez AP, Rustin P: Succinate dehydrogenase deficiency in human. Cell Mol Life Sci. 2005 Oct;62(19-20):2317-24. [PubMed:16143825 ]
  2. Rustin P, Rotig A: Inborn errors of complex II--unusual human mitochondrial diseases. Biochim Biophys Acta. 2002 Jan 17;1553(1-2):117-22. [PubMed:11803021 ]
  3. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  4. 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 ]
  5. 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 ]
  6. 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 ]
  7. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.