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Showing metabocard for Methyl pentanoate (HMDB0031207)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:41:37 UTC
Update Date2023-02-21 17:20:03 UTC
HMDB IDHMDB0031207
Secondary Accession Numbers
  • HMDB31207
Metabolite Identification
Common NameMethyl pentanoate
DescriptionMethyl pentanoate, also known as fema 2752 or methyl N-valerate, belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group. Methyl pentanoate is the ester formed by the condensation of pentanoic acid and methanol. Methyl pentanoate is a very hydrophobic molecule, practically insoluble in water, and relatively neutral.
Structure
Data?1677000003
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031207 (Methyl pentanoate)

  Mrv1652303202019002D          

  8  7  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  2  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
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3D MOL for HMDB0031207 (Methyl pentanoate)

HMDB0031207
     RDKit          3D
Methyl pentanoate
 20 19  0  0  0  0  0  0  0  0999 V2000
   -3.0081    0.2066    0.4624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6845   -0.4653    0.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9746    0.3792   -0.8912 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3539   -0.1620   -1.3300 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3055   -0.3096   -0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1033   -0.9437    0.8253 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5854    0.2889   -0.3079 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5184    0.1559    0.7568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8736    1.3151    0.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8206   -0.0607   -0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2663    0.0691    1.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9358   -1.4270   -0.4311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1337   -0.7324    1.0024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6529    0.4123   -1.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8227    1.4304   -0.5442 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7834    0.5778   -2.0709 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2445   -1.1031   -1.9295 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4303    1.0119    1.4813 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5209    0.1026    0.3111 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3270   -0.7458    1.3759 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  2  0
  5  7  1  0
  7  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  8 18  1  0
  8 19  1  0
  8 20  1  0
M  END
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3D SDF for HMDB0031207 (Methyl pentanoate)

  Mrv1652303202019002D          

  8  7  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  2  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031207

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O2/c1-3-4-5-6(7)8-2/h3-5H2,1-2H3

> <INCHI_KEY>
HNBDRPTVWVGKBR-UHFFFAOYSA-N

> <FORMULA>
C6H12O2

> <MOLECULAR_WEIGHT>
116.1583

> <EXACT_MASS>
116.083729628

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.336584748694637

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl pentanoate

> <ALOGPS_LOGP>
1.75

> <JCHEM_LOGP>
1.5122215186666668

> <ALOGPS_LOGS>
-1.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.023978858710616

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
31.2417

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.51e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl valerate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031207 (Methyl pentanoate)

HMDB0031207
     RDKit          3D
Methyl pentanoate
 20 19  0  0  0  0  0  0  0  0999 V2000
   -3.0081    0.2066    0.4624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6845   -0.4653    0.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9746    0.3792   -0.8912 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3539   -0.1620   -1.3300 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3055   -0.3096   -0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1033   -0.9437    0.8253 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5854    0.2889   -0.3079 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5184    0.1559    0.7568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8736    1.3151    0.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8206   -0.0607   -0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2663    0.0691    1.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9358   -1.4270   -0.4311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1337   -0.7324    1.0024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6529    0.4123   -1.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8227    1.4304   -0.5442 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7834    0.5778   -2.0709 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2445   -1.1031   -1.9295 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4303    1.0119    1.4813 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5209    0.1026    0.3111 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3270   -0.7458    1.3759 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  2  0
  5  7  1  0
  7  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  8 18  1  0
  8 19  1  0
  8 20  1  0
M  END
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PDB for HMDB0031207 (Methyl pentanoate)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       9.955   2.667   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    8                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    2    6                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0031207 (Methyl pentanoate)

COMPND    HMDB0031207
HETATM    1  C1  UNL     1      -3.008   0.207   0.462  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.685  -0.465   0.110  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.975   0.379  -0.891  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.354  -0.162  -1.330  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.305  -0.310  -0.236  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.103  -0.944   0.825  1.00  0.00           O  
HETATM    7  O2  UNL     1       2.585   0.289  -0.308  1.00  0.00           O  
HETATM    8  C6  UNL     1       3.518   0.156   0.757  1.00  0.00           C  
HETATM    9  H1  UNL     1      -2.874   1.315   0.338  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.821  -0.061  -0.238  1.00  0.00           H  
HETATM   11  H3  UNL     1      -3.266   0.069   1.524  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.936  -1.427  -0.431  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.134  -0.732   1.002  1.00  0.00           H  
HETATM   14  H6  UNL     1      -1.653   0.412  -1.798  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.823   1.430  -0.544  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.783   0.578  -2.071  1.00  0.00           H  
HETATM   17  H9  UNL     1       0.244  -1.103  -1.930  1.00  0.00           H  
HETATM   18  H10 UNL     1       3.430   1.012   1.481  1.00  0.00           H  
HETATM   19  H11 UNL     1       4.521   0.103   0.311  1.00  0.00           H  
HETATM   20  H12 UNL     1       3.327  -0.746   1.376  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3   12   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6    6    7
CONECT    7    8
CONECT    8   18   19   20
END
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SMILES for HMDB0031207 (Methyl pentanoate)

CCCCC(=O)OC
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INCHI for HMDB0031207 (Methyl pentanoate)

InChI=1S/C6H12O2/c1-3-4-5-6(7)8-2/h3-5H2,1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Methyl pentanoic acidGenerator
FEMA 2752HMDB
Methyl ester OF pentanoic acidHMDB
Methyl N-valerateHMDB
Methyl valerateHMDB
Methyl valerianateHMDB
N-Valeric acid methyl esterHMDB
Pentanoic acid, methyl esterHMDB
Valeric acid methyl esterHMDB
Valeric acid, methyl esterHMDB
Chemical FormulaC6H12O2
Average Molecular Weight116.1583
Monoisotopic Molecular Weight116.083729628
IUPAC Namemethyl pentanoate
Traditional Namemethyl valerate
CAS Registry Number624-24-8
SMILES
CCCCC(=O)OC
InChI Identifier
InChI=1S/C6H12O2/c1-3-4-5-6(7)8-2/h3-5H2,1-2H3
InChI KeyHNBDRPTVWVGKBR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acid esters
Direct ParentFatty acid methyl esters
Alternative Parents
Substituents
  • Fatty acid methyl ester
  • Methyl ester
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • 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
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point118.00 to 119.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility5.06 mg/mL at 25 °CNot Available
LogP1.96Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Nonalcoholic fatty liver disease
  1. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]
Diarrhoea predominant irritable bowel syndrome
  1. Ahmed I, Greenwood R, Costello Bde L, Ratcliffe NM, Probert CS: An investigation of fecal volatile organic metabolites in irritable bowel syndrome. PLoS One. 2013;8(3):e58204. doi: 10.1371/journal.pone.0058204. Epub 2013 Mar 13. [PubMed:23516449 ]
Autism
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Pervasive developmental disorder not otherwise specified
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Crohn's disease
  1. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Ulcerative colitis
  1. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB003229
KNApSAcK IDC00053483
Chemspider ID11706
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethyl pentanoate
METLIN IDNot Available
PubChem Compound12206
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1008901
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.