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Showing NP-Card for Isocaproic acid (NP0000395)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:58:04 UTC
NP-MRD IDNP0000395
Secondary Accession NumbersNone
Natural Product Identification
Common NameIsocaproic acid
DescriptionIsocaproic acid, a metabolite of 20 alpha-hydroxycholesterol (PMID 14446007 ) and is an important metabolite in early placentas enabling the convertion from cholesterol to pregnenolone to Dehydroepiandrosterone (DHEA) (PMID 11972299 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000395 (Isocaproic acid)


  Mrv1652305271900172D          

  8  7  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
Download

3D MOL for NP0000395 (Isocaproic acid)

HMDB0000689
     RDKit          3D
Isocaproic acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.2393    1.0867   -0.9743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0261   -0.3588   -0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3137   -0.8999   -0.0243 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0980   -0.4106    0.4531 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3405    0.1691   -0.2277 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4998    0.1689    0.6792 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3640   -0.2749    1.8378 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7305    0.6436    0.2882 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2611    1.2109   -1.3842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5062    1.3082   -1.7758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0414    1.7664   -0.1162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7452   -0.9149   -1.4920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8613   -1.4190   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1044   -1.6642    0.7495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9893   -0.1484    0.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2051    0.2354    1.3010 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2987   -1.4530    0.7715 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1406    1.2020   -0.5773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5260   -0.4423   -1.1481 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2949    0.1949   -0.4393 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  8 20  1  0
M  END
Download

3D SDF for NP0000395 (Isocaproic acid)


  Mrv1652305271900172D          

  8  7  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000395

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O2/c1-5(2)3-4-6(7)8/h5H,3-4H2,1-2H3,(H,7,8)

> <INCHI_KEY>
FGKJLKRYENPLQH-UHFFFAOYSA-N

> <FORMULA>
C6H12O2

> <MOLECULAR_WEIGHT>
116.1583

> <EXACT_MASS>
116.083729628

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.062697113252494

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-methylpentanoic acid

> <ALOGPS_LOGP>
1.72

> <JCHEM_LOGP>
1.6533465589999996

> <ALOGPS_LOGS>
-0.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.090081586138642

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
31.0212

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.29e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isocaproate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0000395 (Isocaproic acid)

HMDB0000689
     RDKit          3D
Isocaproic acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.2393    1.0867   -0.9743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0261   -0.3588   -0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3137   -0.8999   -0.0243 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0980   -0.4106    0.4531 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3405    0.1691   -0.2277 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4998    0.1689    0.6792 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3640   -0.2749    1.8378 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7305    0.6436    0.2882 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2611    1.2109   -1.3842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5062    1.3082   -1.7758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0414    1.7664   -0.1162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7452   -0.9149   -1.4920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8613   -1.4190   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1044   -1.6642    0.7495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9893   -0.1484    0.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2051    0.2354    1.3010 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2987   -1.4530    0.7715 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1406    1.2020   -0.5773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5260   -0.4423   -1.1481 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2949    0.1949   -0.4393 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  8 20  1  0
M  END
Download

PDB for NP0000395 (Isocaproic 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      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.976   3.644   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
Download

3D PDB for NP0000395 (Isocaproic acid)

COMPND    HMDB0000689
HETATM    1  C1  UNL     1      -1.239   1.087  -0.974  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.026  -0.359  -0.574  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.314  -0.900  -0.024  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.098  -0.411   0.453  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.340   0.169  -0.228  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.500   0.169   0.679  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.364  -0.275   1.838  1.00  0.00           O  
HETATM    8  O2  UNL     1       3.731   0.644   0.288  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.261   1.211  -1.384  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.506   1.308  -1.776  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.041   1.766  -0.116  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.745  -0.915  -1.492  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.861  -1.419  -0.855  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.104  -1.664   0.749  1.00  0.00           H  
HETATM   15  H7  UNL     1      -2.989  -0.148   0.385  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.205   0.235   1.301  1.00  0.00           H  
HETATM   17  H9  UNL     1       0.299  -1.453   0.771  1.00  0.00           H  
HETATM   18  H10 UNL     1       1.141   1.202  -0.577  1.00  0.00           H  
HETATM   19  H11 UNL     1       1.526  -0.442  -1.148  1.00  0.00           H  
HETATM   20  H12 UNL     1       4.295   0.195  -0.439  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    4   12
CONECT    3   13   14   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7    7    8
CONECT    8   20
END
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SMILES for NP0000395 (Isocaproic acid)

CC(C)CCC(O)=O
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INCHI for NP0000395 (Isocaproic acid)

InChI=1S/C6H12O2/c1-5(2)3-4-6(7)8/h5H,3-4H2,1-2H3,(H,7,8)
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View in JSmol
Synonyms
ValueSource
4,4-Dimethylbutanoic acidChEBI
4-Methyl-N-valeric acidChEBI
4-Methyl-pentanoic acidChEBI
4-Methyl-valeric acidChEBI
4-Methylvaleric acidChEBI
Isobutylacetic acidChEBI
Isohexanoic acidChEBI
Isohexoic acidChEBI
4,4-DimethylbutanoateGenerator
4-Methyl-N-valerateGenerator
4-Methyl-pentanoateGenerator
4-Methyl-valerateGenerator
4-MethylvalerateGenerator
IsobutylacetateGenerator
IsohexanoateGenerator
IsohexoateGenerator
IsocaproateGenerator
4-MethylpentanoateHMDB
4-Methylpentanoic acidHMDB
Isocaproic acid, sodium saltHMDB
4-Methyl valerateHMDB
Isocaproic acidMeSH
Chemical FormulaC6H12O2
Average Mass116.1583 Da
Monoisotopic Mass116.08373 Da
IUPAC Name4-methylpentanoic acid
Traditional Nameisocaproate
CAS Registry Number646-07-1
SMILES
CC(C)CCC(O)=O
InChI Identifier
InChI=1S/C6H12O2/c1-5(2)3-4-6(7)8/h5H,3-4H2,1-2H3,(H,7,8)
InChI KeyFGKJLKRYENPLQH-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, CDCl3, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Amorphophallus elatusLOTUS Database
Ananas comosusFooDB
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
Capsicum annuumFooDB
Capsicum annuum var. annuumFooDB
CervidaeFooDB
Cervus canadensisFooDB
Citrus X sinensis (L.) Osbeck (pro. sp.)FooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
Pelargonium graveolensLOTUS Database
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMethyl-branched fatty acids
Alternative Parents
Substituents
  • Methyl-branched fatty acid
  • Monocarboxylic 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
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point-33 °CNot Available
Boiling Point199.00 to 201.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility5266 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.560 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility12.9 g/LALOGPS
logP1.72ALOGPS
logP1.65ChemAxon
logS-0.96ALOGPS
pKa (Strongest Acidic)5.09ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity31.02 m³·mol⁻¹ChemAxon
Polarizability13.06 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000689
DrugBank IDDB03993
Phenol Explorer Compound IDNot Available
FoodDB IDFDB008206
KNApSAcK IDC00050474
Chemspider ID12067
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link4-Methylpentanoic acid
METLIN ID4191
PubChem Compound12587
PDB IDNot Available
ChEBI ID74903
Good Scents IDrw1036331
References
General References
  1. SHIMIZU K, DORFMAN RI, GUT M: Isocaproic acid, a metabolite of 20 alpha-hydroxycholesterol. J Biol Chem. 1960 Jun;235:PC25. [PubMed:14446007 ]
  2. Loganath A, Peh KL, Wong PC: Evidence for the biosynthesis of DHEA from cholesterol by first-trimester human placental tissue: source of androgens. Horm Metab Res. 2002 Mar;34(3):116-20. [PubMed:11972299 ]
  3. Zietek M, Celewicz Z, Kikut J, Szczuko M: Implications of SCFAs on the Parameters of the Lipid and Hepatic Profile in Pregnant Women. Nutrients. 2021 May 21;13(6). pii: nu13061749. doi: 10.3390/nu13061749. [PubMed:34063900 ]
  4. Ratajczak W, Mizerski A, Ryl A, Slojewski M, Sipak O, Piasecka M, Laszczynska M: Alterations in fecal short chain fatty acids (SCFAs) and branched short-chain fatty acids (BCFAs) in men with benign prostatic hyperplasia (BPH) and metabolic syndrome (MetS). Aging (Albany NY). 2021 Apr 13;13(8):10934-10954. doi: 10.18632/aging.202968. Epub 2021 Apr 13. [PubMed:33847600 ]
  5. Weng YJ, Gan HY, Li X, Huang Y, Li ZC, Deng HM, Chen SZ, Zhou Y, Wang LS, Han YP, Tan YF, Song YJ, Du ZM, Liu YY, Wang Y, Qin N, Bai Y, Yang RF, Bi YJ, Zhi FC: Correlation of diet, microbiota and metabolite networks in inflammatory bowel disease. J Dig Dis. 2019 Sep;20(9):447-459. doi: 10.1111/1751-2980.12795. Epub 2019 Aug 1. [PubMed:31240835 ]
  6. McCafferty KW, Bedford MR, Kerr BJ, Dozier WA: Effects of age and supplemental xylanase in corn- and wheat-based diets on cecal volatile fatty acid concentrations of broilers1. Poult Sci. 2019 Oct 1;98(10):4787-4800. doi: 10.3382/ps/pez194. [PubMed:31065717 ]
  7. Skonieczna-Zydecka K, Grochans E, Maciejewska D, Szkup M, Schneider-Matyka D, Jurczak A, Loniewski I, Kaczmarczyk M, Marlicz W, Czerwinska-Rogowska M, Pelka-Wysiecka J, Dec K, Stachowska E: Faecal Short Chain Fatty Acids Profile is Changed in Polish Depressive Women. Nutrients. 2018 Dec 7;10(12). pii: nu10121939. doi: 10.3390/nu10121939. [PubMed:30544489 ]
  8. Authors unspecified: Erratum: Effects of Alpha-hydroxy-isocaproic acid upon Body Composition in a Type I Diabetic Patient with Muscle Atrophy - A Case Study. Yale J Biol Med. 2018 Dec 7;91(3):355. eCollection 2018 Sep. [PubMed:30534025 ]
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