Showing NP-Card for Pimelic acid (NP0001322)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2025-02-11 15:43:43 UTC
NP-MRD IDNP0001322
Natural Product DOIhttps://doi.org/10.57994/1430
Secondary Accession NumbersNone
Natural Product 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001322 (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
Download

3D MOL for NP0001322 (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 NP0001322 (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>
NP0001322

> <DATABASE_NAME>
NP-MRD

> <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 NP0001322 (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

PDB for NP0001322 (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
Download

3D PDB for NP0001322 (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
Download

SMILES for NP0001322 (Pimelic acid)

OC(=O)CCCCCC(O)=O
Download

INCHI for NP0001322 (Pimelic acid)

InChI=1S/C7H12O4/c8-6(9)4-2-1-3-5-7(10)11/h1-5H2,(H,8,9)(H,10,11)
Download
View in JSmol
Synonyms
Chemical FormulaC7H12O4
Average Mass160.1678 Da
Monoisotopic Mass160.07356 Da
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
Experimental Spectra
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600.133705802, CD3OD, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-02View Spectrum
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
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
Physical Properties
StateSolid
Experimental 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 CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted 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
HMDB IDHMDB0000857
DrugBank IDDB01856
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDrw1274891
References
General References
  1. 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 ]
  2. Pettit BR: The analysis of thiodiglycollic acid by selected ion monitoring. Clin Chim Acta. 1986 Apr 15;156(1):85-90. [PubMed:3698320 ]
  3. 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 ]
  4. 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 ]
  5. 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 ]
  6. 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 ]
  7. 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 ]