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Showing metabocard for Pimelic acid (HMDB0000857)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:14 UTC
HMDB IDHMDB0000857
Secondary Accession Numbers
  • HMDB00857
Metabolite Identification
Common NamePimelic acid
DescriptionPimelic acid, also known as heptanedioic acid is a dicarboxylic acid. Derivatives of pimelic acid are involved in the biosynthesis of the amino acid called lysine. Pimelic acid is one methylene longer than a related dicarboxylic acid, adipic acid, a precursor to many polyesters and polyamides. Pimelic acid is essential for the synthesis of biotin (also called vitamin B7). Biotin is a heterocyclic, S-containing monocarboxylic acid that is made from two precursors, alanine and pimeloyl-CoA. Biotin is important in fatty acid synthesis, branched-chain amino acid catabolism, and gluconeogenesis. Biotin is found in a wide range of foods. Likewise, intestinal bacteria synthesize biotin, which is then absorbed by the host animal. Pimelic acid (which is the precursor for pimeloyl-CoA) is synthesized in many bacteria via a head-to-tail incorporation of acetate units through a modified fatty acid synthetic pathway using O-methyl esters disguised to resemble the canonical intermediates of the fatty acid synthetic pathway (PMID:21435937 ). Some bacteria and yeast synthesize pimelic acid not by biosynthesis, but via cleavage of longer chain fatty acids (such as linolenic acid) via a cytochrome P450-like enzyme (PMID:28196402 , 21435937 , 3236079 ). Pimelic acid is excreted in elevated amounts in the urine of individuals with mitochondrial beta-oxidation disorders and peroxisomal beta oxidation disorders (PMID:1527989 )
Structure
Data?1676999714
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000857 (Pimelic acid)


  Mrv1652305271900262D          

 11 10  0  0  0  0            999 V2000
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  END
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3D MOL for HMDB0000857 (Pimelic acid)

HMDB0000857
     RDKit          3D
Pimelic acid
 23 22  0  0  0  0  0  0  0  0999 V2000
    2.4459    1.4973   -0.3925 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0884    0.4275   -0.3197 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3959    0.4122   -0.7669 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4569   -0.7846    0.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0400   -0.6157    0.6568 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0813   -0.2076   -0.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2971   -0.1020    0.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2744    0.3129   -0.8148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6445    0.4447   -0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5681    0.7831   -1.0467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8643    0.1931    1.0665 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1725    0.3452   -0.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0161   -1.1495    1.1437 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5322   -1.6369   -0.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9223    0.0843    1.5091 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6817   -1.6073    1.0555 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2783    0.7907   -0.8093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0464   -0.9715   -1.2033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6050   -1.1079    0.6399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2053    0.6459    1.0690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2241   -0.4353   -1.6229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9417    1.2830   -1.2248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4407    0.6797    1.8298 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  2  0
  9 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
M  END
Download

3D SDF for HMDB0000857 (Pimelic acid)


  Mrv1652305271900262D          

 11 10  0  0  0  0            999 V2000
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000857

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O4/c8-6(9)4-2-1-3-5-7(10)11/h1-5H2,(H,8,9)(H,10,11)

> <INCHI_KEY>
WLJVNTCWHIRURA-UHFFFAOYSA-N

> <FORMULA>
C7H12O4

> <MOLECULAR_WEIGHT>
160.1678

> <EXACT_MASS>
160.073558872

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.309765941205747

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
heptanedioic acid

> <ALOGPS_LOGP>
0.51

> <JCHEM_LOGP>
0.9352230276666667

> <ALOGPS_LOGS>
-1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.8101291244285145

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.045044284282043

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
37.339999999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.33e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pimelic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000857 (Pimelic acid)

HMDB0000857
     RDKit          3D
Pimelic acid
 23 22  0  0  0  0  0  0  0  0999 V2000
    2.4459    1.4973   -0.3925 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0884    0.4275   -0.3197 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3959    0.4122   -0.7669 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4569   -0.7846    0.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0400   -0.6157    0.6568 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0813   -0.2076   -0.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2971   -0.1020    0.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2744    0.3129   -0.8148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6445    0.4447   -0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5681    0.7831   -1.0467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8643    0.1931    1.0665 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1725    0.3452   -0.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0161   -1.1495    1.1437 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5322   -1.6369   -0.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9223    0.0843    1.5091 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6817   -1.6073    1.0555 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2783    0.7907   -0.8093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0464   -0.9715   -1.2033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6050   -1.1079    0.6399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2053    0.6459    1.0690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2241   -0.4353   -1.6229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9417    1.2830   -1.2248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4407    0.6797    1.8298 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  2  0
  9 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
M  END
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PDB for HMDB0000857 (Pimelic acid)

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      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.596   4.771   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       6.930   2.461   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0000857 (Pimelic acid)

COMPND    HMDB0000857
HETATM    1  O1  UNL     1       2.446   1.497  -0.393  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.088   0.428  -0.320  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.396   0.412  -0.767  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.457  -0.785   0.232  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.040  -0.616   0.657  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.081  -0.208  -0.406  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.297  -0.102   0.264  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.274   0.313  -0.815  1.00  0.00           C  
HETATM    9  C7  UNL     1      -3.644   0.445  -0.270  1.00  0.00           C  
HETATM   10  O3  UNL     1      -4.568   0.783  -1.047  1.00  0.00           O  
HETATM   11  O4  UNL     1      -3.864   0.193   1.066  1.00  0.00           O  
HETATM   12  H1  UNL     1       5.172   0.345  -0.103  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.016  -1.149   1.144  1.00  0.00           H  
HETATM   14  H3  UNL     1       2.532  -1.637  -0.486  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.922   0.084   1.509  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.682  -1.607   1.056  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.278   0.791  -0.809  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.046  -0.972  -1.203  1.00  0.00           H  
HETATM   19  H8  UNL     1      -1.605  -1.108   0.640  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.205   0.646   1.069  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.224  -0.435  -1.623  1.00  0.00           H  
HETATM   22  H11 UNL     1      -1.942   1.283  -1.225  1.00  0.00           H  
HETATM   23  H12 UNL     1      -3.441   0.680   1.830  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5   13   14
CONECT    5    6   15   16
CONECT    6    7   17   18
CONECT    7    8   19   20
CONECT    8    9   21   22
CONECT    9   10   10   11
CONECT   11   23
END
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SMILES for HMDB0000857 (Pimelic acid)

OC(=O)CCCCCC(O)=O
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INCHI for HMDB0000857 (Pimelic acid)

InChI=1S/C7H12O4/c8-6(9)4-2-1-3-5-7(10)11/h1-5H2,(H,8,9)(H,10,11)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,5-Pentanedicarboxylic acidChEBI
6-Carboxyhexanoic acidChEBI
Heptanedioic acidChEBI
PimelateChEBI
6-CarboxyhexanoateKegg
1,5-PentanedicarboxylateGenerator
HeptanedioateGenerator
Acid, pimelicHMDB
Acids, pimelicHMDB
Pimelic acidsHMDB
1,7-HeptanedioateHMDB
1,7-Heptanedioic acidHMDB
HeptandioateHMDB
Heptandioic acidHMDB
Heptane-1,7-dioateHMDB
Heptane-1,7-dioic acidHMDB
PilerateHMDB
Pileric acidHMDB
Chemical FormulaC7H12O4
Average Molecular Weight160.1678
Monoisotopic Molecular Weight160.073558872
IUPAC Nameheptanedioic acid
Traditional Namepimelic acid
CAS Registry Number111-16-0
SMILES
OC(=O)CCCCCC(O)=O
InChI Identifier
InChI=1S/C7H12O4/c8-6(9)4-2-1-3-5-7(10)11/h1-5H2,(H,8,9)(H,10,11)
InChI KeyWLJVNTCWHIRURA-UHFFFAOYSA-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
  • 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 Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point103 - 106 °CNot Available
Boiling Point342.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility50 mg/mLNot Available
LogP0.61HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg129.28630932474
[M-H]-Not Available130.8http://allccs.zhulab.cn/database/detail?ID=AllCCS00000223
Predicted Molecular Properties
PropertyValueSource
Water Solubility13.3 g/LALOGPS
logP0.51ALOGPS
logP0.94ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)4.05ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity37.34 m³·mol⁻¹ChemAxon
Polarizability16.31 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+136.43231661259
DarkChem[M-H]-132.39131661259
AllCCS[M+H]+135.87232859911
AllCCS[M-H]-134.63732859911
DeepCCS[M+H]+133.89730932474
DeepCCS[M-H]-130.54330932474
DeepCCS[M-2H]-167.11730932474
DeepCCS[M+Na]+142.51630932474
AllCCS[M+H]+135.932859911
AllCCS[M+H-H2O]+132.032859911
AllCCS[M+NH4]+139.532859911
AllCCS[M+Na]+140.632859911
AllCCS[M-H]-134.632859911
AllCCS[M+Na-2H]-136.532859911
AllCCS[M+HCOO]-138.532859911

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, 2022.3.35 minutes32390414
Predicted by Siyang on May 30, 20229.742 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.68 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid116.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1299.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid287.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid99.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid179.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid134.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid286.9 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 Acid335.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)129.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid740.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid280.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid947.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid216.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid255.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate536.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA216.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water372.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Pimelic acidOC(=O)CCCCCC(O)=O2289.4Standard polar33892256
Pimelic acidOC(=O)CCCCCC(O)=O1254.1Standard non polar33892256
Pimelic acidOC(=O)CCCCCC(O)=O1471.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pimelic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)CCCCCC(=O)O1511.5Semi standard non polar33892256
Pimelic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)CCCCCC(=O)O[Si](C)(C)C1616.9Semi standard non polar33892256
Pimelic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCCCC(=O)O1752.6Semi standard non polar33892256
Pimelic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCCCC(=O)O[Si](C)(C)C(C)(C)C2070.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Pimelic acid GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-056s-1910000000-58bf29a41b2e4b405df92014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pimelic acid EI-B (Non-derivatized)splash10-0r7l-9100000000-aeff5d9828ac92b330282017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pimelic acid EI-B (Non-derivatized)splash10-054k-1910000000-fc6cb63b081b4f5f7fd32017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pimelic acid GC-EI-TOF (Non-derivatized)splash10-056s-1910000000-58bf29a41b2e4b405df92017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pimelic acid GC-EI-TOF (Non-derivatized)splash10-054k-1900000000-403538c5b4091abf0a3d2017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pimelic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9400000000-3bc5f898da696375482f2017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pimelic acid GC-MS (2 TMS) - 70eV, Positivesplash10-00y0-9720000000-f599c8c7e2d374dc1d0c2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pimelic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pimelic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pimelic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pimelic acid GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid Quattro_QQQ 10V, Negative-QTOF (Annotated)splash10-0002-9300000000-a3d2b3924fcede41e3312012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid Quattro_QQQ 25V, Negative-QTOF (Annotated)splash10-0002-9100000000-7050dc1518d598ad50512012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid Quattro_QQQ 40V, Negative-QTOF (Annotated)splash10-052e-9200000000-84550d0cfeb05e8d79bd2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid EI-B (Unknown) , Positive-QTOFsplash10-0r7l-9100000000-b698134a5d1e523a961e2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative-QTOFsplash10-0a4i-0900000000-a3b877a40a98e4d079932012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative-QTOFsplash10-0002-9500000000-6f90176eaadac29eae282012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative-QTOFsplash10-0002-9000000000-859f1028218d04c20dc62012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative-QTOFsplash10-0002-9000000000-ef436118494b323530f42012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative-QTOFsplash10-0002-9000000000-15fa4059d8c10e1e3a032012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ , negative-QTOFsplash10-0a4i-0900000000-a3b877a40a98e4d079932017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ , negative-QTOFsplash10-0002-9500000000-6f90176eaadac29eae282017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ , negative-QTOFsplash10-0002-9000000000-0ece97699a3ecbbd29c52017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ , negative-QTOFsplash10-0002-9000000000-aa9d7a3b0b034eb999ac2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid LC-ESI-QQ , negative-QTOFsplash10-0002-9000000000-15fa4059d8c10e1e3a032017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid 20V, Negative-QTOFsplash10-0002-9100000000-bbaaf04acf7504d9af122021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid 40V, Negative-QTOFsplash10-0006-9000000000-2467588398a0cc1a71732021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid 40V, Negative-QTOFsplash10-0ufr-9000000000-2c0303cc46347643edee2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid 20V, Negative-QTOFsplash10-0002-9200000000-62e7353cf7ec99f7b2572021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pimelic acid 10V, Negative-QTOFsplash10-0002-9700000000-51105e097da7cfc85c562021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pimelic acid 10V, Positive-QTOFsplash10-03dl-1900000000-f72d396c48eae140d2ea2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pimelic acid 20V, Positive-QTOFsplash10-02tc-6900000000-148d1369a6cc8216a4d42017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pimelic acid 40V, Positive-QTOFsplash10-0aou-9000000000-8148e8a28ecc0a5f18192017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pimelic acid 10V, Negative-QTOFsplash10-0a4i-0900000000-97c3b22812cb1495f92e2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pimelic acid 20V, Negative-QTOFsplash10-0a4i-2900000000-ec8e65ccb8032a2fffa02017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pimelic acid 40V, Negative-QTOFsplash10-0a4l-9100000000-c8c106238d3a22f75dbc2017-07-26Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart 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 Locations
  • Membrane
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.21 (0.11-0.31) uMInfant (0-1 year old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.53-0.92 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified0-3.6 umol/mmol creatinineInfant (0-1 year old)Female
Normal		 details
UrineDetected and Quantified0-2.0 umol/mmol creatinineInfant (0-1 year old)Male
Normal		 details
UrineDetected and Quantified0-1.8 umol/mmol creatinineInfant (0-1 year old)Female
Normal		 details
UrineDetected and Quantified0-1.3 umol/mmol creatinineInfant (0-1 year old)Male
Normal		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified2.4 (0.1-33.5) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified0.61-1.2 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified4.011 +/- 3.319 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Analysis of 30 no...
 details
UrineDetected and Quantified6.371 +/- 2.576 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Analysis of 30 no...
 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified2.2 (0.7-4.0) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified1.9 (0.5-3.5) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified15.8 +/- 2.4 umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected and Quantified2.2 (0.8-11.6) umol/mmol creatinineChildren (1-13 years old)Both
Normal		 details
UrineDetected and Quantified3.6 (1.4-7.4) umol/mmol creatinineChildren (1-13 years old)Both
Normal		 details
UrineDetected and Quantified2.2 (0.1-7.1) umol/mmol creatinineChildren (1-13 years old)Both
Normal		 details
UrineDetected and Quantified0.1 umol/mmol creatinineInfant (0-1 year old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.68-12.7 uMInfant (0-1 year old)Female3-Hydroxydicarboxylic aciduria details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected and Quantified22.73 +/- 4.00 umol/mmol creatinineChildren (1-13 years old)BothMalnutrition (type kwashiorkor and marasmus) details
UrineDetected and Quantified7.664 +/- 7.255 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 details
UrineDetected and Quantified2.507 +/- 2.054 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 details
UrineDetected and Quantified2.343 +/- 3.004 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Gastroesophageal reflux disease
    • Analysis of 30 no...
 details
Associated Disorders and Diseases
Disease References
3-Hydroxydicarboxylic aciduria
  1. Hagenfeldt L, von Dobeln U, Holme E, Alm J, Brandberg G, Enocksson E, Lindeberg L: 3-Hydroxydicarboxylic aciduria--a fatty acid oxidation defect with severe prognosis. J Pediatr. 1990 Mar;116(3):387-92. [PubMed:2308028 ]
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDDB01856
Phenol Explorer Compound IDNot Available
FooDB IDFDB022283
KNApSAcK IDC00001199
Chemspider ID376
KEGG Compound IDC02656
BioCyc IDCPD-205
BiGG IDNot Available
Wikipedia LinkPimelic_acid
METLIN ID3280
PubChem Compound385
PDB IDNot Available
ChEBI ID30531
Food Biomarker OntologyNot Available
VMH IDPIME
MarkerDB IDMDB00000268
Good Scents IDrw1274891
References
Synthesis ReferenceMurib, Jawad H.; Kahn, John H. Production of pimelic acid by carbonylation of e-caprolactone using excess water. U.S. (1989), 3 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
  2. Passi S, Picardo M, Mingrone G, Breathnach AS, Nazzaro-Porro M: Azelaic acid--biochemistry and metabolism. Acta Derm Venereol Suppl (Stockh). 1989;143:8-13. [PubMed:2505463 ]
  3. Pettit BR: The analysis of thiodiglycollic acid by selected ion monitoring. Clin Chim Acta. 1986 Apr 15;156(1):85-90. [PubMed:3698320 ]
  4. Niwa T, Ohki T, Maeda K, Saito A, Kobayashi K: Pattern of aliphatic dicarboxylic acids in uremic serum including a new organic acid, 2,4-dimethyladipic acid. Clin Chim Acta. 1979 Nov 15;99(1):71-83. [PubMed:498544 ]
  5. Mahadevappa VG, Holub BJ: The molecular species composition of individual diacyl phospholipids in human platelets. Biochim Biophys Acta. 1982 Oct 14;713(1):73-9. [PubMed:7138900 ]
  6. Cronan JE, Lin S: Synthesis of the alpha,omega-dicarboxylic acid precursor of biotin by the canonical fatty acid biosynthetic pathway. Curr Opin Chem Biol. 2011 Jun;15(3):407-13. doi: 10.1016/j.cbpa.2011.03.001. Epub 2011 Mar 23. [PubMed:21435937 ]
  7. Manandhar M, Cronan JE: Pimelic acid, the first precursor of the Bacillus subtilis biotin synthesis pathway, exists as the free acid and is assembled by fatty acid synthesis. Mol Microbiol. 2017 May;104(4):595-607. doi: 10.1111/mmi.13648. Epub 2017 Mar 3. [PubMed:28196402 ]
  8. Ohsugi M, Miyauchi K, Tachibana K, Nakao S: Formation of a biotin precursor, pimelic acid, in yeasts from C18 fatty acids. J Nutr Sci Vitaminol (Tokyo). 1988 Aug;34(4):343-52. doi: 10.3177/jnsv.34.343. [PubMed:3236079 ]
  9. Bennett MJ, Ragni MC, Hood I, Hale DE: Azelaic and pimelic acids: metabolic intermediates or artefacts? J Inherit Metab Dis. 1992;15(2):220-3. doi: 10.1007/BF01799635. [PubMed:1527989 ]