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Showing NP-Card for 2-Tridecanone (NP0047872)

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Record Information
Version2.0
Created at2022-03-17 20:47:21 UTC
Updated at2024-09-03 04:16:41 UTC
NP-MRD IDNP0047872
Natural Product DOIhttps://doi.org/10.57994/0759
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Tridecanone
Description2-Tridecanone, also known as NSC 14763 or fema 3388, belongs to the class of organic compounds known as ketones. These are organic compounds in which a carbonyl group is bonded to two carbon atoms R2C=O (neither R may be a hydrogen atom). Ketones that have one or more alpha-hydrogen atoms undergo keto-enol tautomerization, the tautomer being an enol. Thus, 2-tridecanone is considered to be an oxygenated hydrocarbon lipid molecule. 2-Tridecanone is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 2-Tridecanone is a coconut, dairy, and earthy tasting compound. Outside of the human body, 2-Tridecanone has been detected, but not quantified in, several different foods, such as garden onions, garden tomato (var.), Citrus, evergreen blackberries, and onion-family vegetables. This could make 2-tridecanone a potential biomarker for the consumption of these foods. 2-Tridecanone, with regard to humans, has been linked to the inborn metabolic disorder celiac disease. Isolated from plant oils, e.G. 2-Tridecanone is found in Bowdichia virgilioides, Cochlospermum tinctorium, Commiphora rostrata, Drosophila buzzatii, Echinacea angustifolia, Esenbeckia yaxhoob Lundell, Etlingera elatior, Evernia prunastri, Acca sellowiana, Frullania solanderiana, Hamamelis virginiana, Hedychium spicatum, Helianthus annuus, Humulus lupulus , Juncus effusus , Nicotiana tabacum , Pilocarpus pauciflorus, Rosa rugosa , Ruta angustifolia, Ruta graveolens, Solanum agrimoniifolium, Solanum habrochaites, Sorbus tianschanica, Vaccinium corymbosum, Vaccinium macrocarpon, Vasconcellea heilbornii, Zanthoxylum ailanthoides, Zanthoxylum armatum , Zanthoxylum dipetalum, Zanthoxylum integrifoliolum, Zanthoxylum zanthoxyloides and Zingiber mioga. 2-Tridecanone was first documented in 2013 (PMID: 23374049). Palm oil, coconut oiland is also found in American cranberry, rabbiteye, blueberry, raspberry, grapefruit, onion, ginger and cheeses.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0047872 (2-Tridecanone)


  Mrv0541 05061307372D          

 14 13  0  0  0  0            999 V2000
    5.4730    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0467    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9020    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6164    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3309    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0454    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7599    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1888    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9033    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6177    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3322    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3322    2.7474    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  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13  2  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  2  0  0  0  0
M  END
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3D MOL for NP0047872 (2-Tridecanone)

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3D SDF for NP0047872 (2-Tridecanone)

  Mrv0541 05061307372D          

 14 13  0  0  0  0            999 V2000
    5.4730    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0467    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9020    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6164    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3309    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0454    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7599    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1888    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9033    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6177    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3322    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3322    2.7474    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  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13  2  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0047872

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCCCC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H26O/c1-3-4-5-6-7-8-9-10-11-12-13(2)14/h3-12H2,1-2H3

> <INCHI_KEY>
CYIFVRUOHKNECG-UHFFFAOYSA-N

> <FORMULA>
C13H26O

> <MOLECULAR_WEIGHT>
198.3449

> <EXACT_MASS>
198.198365454

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
26.895790136217222

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
tridecan-2-one

> <ALOGPS_LOGP>
5.22

> <JCHEM_LOGP>
4.807933640333334

> <ALOGPS_LOGS>
-5.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.64344776069631

> <JCHEM_PKA_STRONGEST_BASIC>
-7.270866249933757

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
62.2307

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.17e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-tridecanone

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0047872 (2-Tridecanone)
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PDB for NP0047872 (2-Tridecanone)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      10.216   7.438   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      26.221   7.438   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.550   6.668   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.884   7.438   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.217   6.668   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      15.551   7.438   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      16.885   6.668   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.218   7.438   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.552   6.668   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      20.886   7.438   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      22.219   6.668   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      23.553   7.438   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.887   6.668   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      24.887   5.128   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2   13                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13    2   12   14                                                  
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

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3D PDB for NP0047872 (2-Tridecanone)
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SMILES for NP0047872 (2-Tridecanone)
CCCCCCCCCCCC(C)=O
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INCHI for NP0047872 (2-Tridecanone)
InChI=1S/C13H26O/c1-3-4-5-6-7-8-9-10-11-12-13(2)14/h3-12H2,1-2H3
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View in JSmol
Synonyms
ValueSource
Hendecyl methyl ketoneChEBI
Methyl N-undecyl ketoneChEBI
Methyl undecyl ketoneChEBI
NSC 14763ChEBI
TridecanoneChEBI
Tridecanone-2ChEBI
2-TridecankjeHMDB
Ammonium palmitateHMDB
FEMA 3388HMDB
Mathyl undecyl kepojeHMDB
Tridecan-2-oneHMDB
2-TridecanoneChEBI
Chemical FormulaC13H26O
Average Mass198.3449 Da
Monoisotopic Mass198.19837 Da
IUPAC Nametridecan-2-one
Traditional Name2-tridecanone
CAS Registry Number593-08-8
SMILES
CCCCCCCCCCCC(C)=O
InChI Identifier
InChI=1S/C13H26O/c1-3-4-5-6-7-8-9-10-11-12-13(2)14/h3-12H2,1-2H3
InChI KeyCYIFVRUOHKNECG-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)bgnzk@missouri.eduNot AvailableNot Available2023-07-28View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)bgnzk@missouri.eduNot AvailableNot Available2023-07-28View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Allium cepaFooDB
    • Mans Boelens, Pieter J. de Valois, Henk J. Wobben, and Arne van der Gen. Volatile Flavor Compound...
Allium fistulosumFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Bowdichia virgilioidesLOTUS Database
Cochlospermum tinctoriumLOTUS Database
Commiphora rostrataLOTUS Database
Drosophila buzzatiiLOTUS Database
Echinacea angustifoliaLOTUS Database
Esenbeckia yaxhoob LundellPlant
Etlingera elatiorLOTUS Database
Evernia prunastriLOTUS Database
Feijoa sellowianaPlant
Frullania solanderianaPlant
Hamamelis virginianaLOTUS Database
Hedychium spicatumLOTUS Database
Helianthus annuusLOTUS Database
Humulus lupulusPlant
Juncus effususPlant
Nicotiana tabacumPlant
Pilocarpus pauciflorusLOTUS Database
Rosa rugosaPlant
Ruta angustifoliaLOTUS Database
Ruta graveolensLOTUS Database
Solanum agrimoniifoliumLOTUS Database
Solanum habrochaitesLOTUS Database
Solanum lycopersicum var. lycopersicumFooDB
Sorbus tianschanicaPlant
Vaccinium corymbosumLOTUS Database
Vaccinium macrocarponLOTUS Database
Vasconcellea x heilborniiLOTUS Database
Zanthoxylum ailanthoidesLOTUS Database
Zanthoxylum armatumPlant
Zanthoxylum dipetalumLOTUS Database
Zanthoxylum integrifoliolumPlant
Zanthoxylum zanthoxyloidesLOTUS Database
Zingiber miogaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ketones. These are organic compounds  in which a carbonyl group is bonded to two carbon atoms R2C=O (neither R may be a hydrogen atom). Ketones that have one or more alpha-hydrogen atoms undergo keto-enol tautomerization, the tautomer being an enol.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct ParentKetones  
Alternative Parents
Substituents
  • Ketone
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP5.22ALOGPS
logP4.81ChemAxon
logS-5.4ALOGPS
pKa (Strongest Acidic)19.64ChemAxon
pKa (Strongest Basic)-7.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity62.23 m³·mol⁻¹ChemAxon
Polarizability26.9 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0034148  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012424  
KNApSAcK IDC00036263  
Chemspider ID11132  
KEGG Compound IDNot Available
BioCyc IDCPD-7901  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11622  
PDB IDNot Available
ChEBI ID77928  
Good Scents IDNot Available
References
General References
  1. Antonious GF: 2-undecanone and 2-tridecanone in field-grown onion. J Environ Sci Health B. 2013;48(4):302-7. doi: 10.1080/03601234.2013.743790. [PubMed:23374049  ]