Showing metabocard for Pimelic acid (MMDBc0000159)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:38:01 UTC
Update Date2024-10-07 02:53:25 UTC
Metabolite IDMMDBc0000159
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923be2a980>


  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 #<Metabolite:0x00007f923be2a980>

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 #<Metabolite:0x00007f923be2a980>


  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>
MMDBc0000159

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f923be2a980>

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 #<Metabolite:0x00007f923be2a980>

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 #<Metabolite:0x00007f923be2a980>

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 #<Metabolite:0x00007f923be2a980>

OC(=O)CCCCCC(O)=O
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INCHI for #<Metabolite:0x00007f923be2a980>

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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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
Molecular FormulaC7H12O4
Average Mass160.1678
Monoisotopic Mass160.073558872
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