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Showing NP-Card for Trimethylamine (NP0000850)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:40:03 UTC
NP-MRD IDNP0000850
Secondary Accession NumbersNone
Natural Product Identification
Common NameTrimethylamine
DescriptionTrimethylamine, also known as NMe3, N(CH3)3, and TMA, is a colorless, hygroscopic, and flammable simple amine with a typical fishy odor in low concentrations and an ammonia like odor in higher concentrations. Trimethylamine has a boiling point of 2.9 Degree centigrade and is a gas at room temperature. Trimethylamine usually comes in pressurized gas cylinders or as a 40% solution in water. Trimethylamine is a nitrogenous base and its positively charged cation is called trimethylammonium cation. A common salt of trimethylamine is trimethylammonium chloride, a hygroscopic colorless solid. Trimethylamine is a product of decomposition of plants and animals. It is the substance mainly responsible for the fishy odor often associated with fouling fish, bacterial vagina infections, and bad breath. It is also associated with taking large doses of choline. Trimethylaminuria is a genetic disorder in which the body is unable to metabolize trimethylamine from food sources. Patients develop a characteristic fish odour of their sweat, urine, and breath after the consumption of choline-rich foods. Trimethylaminuria is an autosomal recessive disorder involving a trimethylamine oxidase deficiency. Trimethylaminuria has also been observed in a certain breed of Rhode Island Red chicken that produces eggs with a fishy smell. Trimethylamine in the urine is a biomarker for the consumption of legumes. It has also been found to be a product of various types of bacteria, such as Achromobacter, Acinetobacter, Actinobacteria, Aeromonas, Alcaligenes, Alteromonas, Anaerococcus, Bacillus, Bacteroides, Bacteroidetes, Burkholderia, Campylobacter, Citrobacter, Clostridium, Desulfitobacterium, Desulfovibrio, Desulfuromonas, Edwardsiella, Enterobacter, Enterococcus, Escherichia, Eubacterium, Firmicutes, Flavobacterium, Gammaproteobacteria, Haloanaerobacter, Klebsiella, Micrococcus, Mobiluncus, Olsenella, Photobacterium, Proteobacteria, Proteus, Providencia, Pseudomonas, Rhodopseudomonas, Ruminococcus, Salmonella, Sarcina, Serratia, Shewanella, Shigella, Sinorhizobium, Sporomusa, Staphylococcus, Stigmatella, Streptococcus, Vibrio and Yokenella (PMID: 26687352 ; PMID: 25108210 ; PMID: 24909875 ; PMID: 28506279 ; PMID: 27190056 ). Trimethylamine is a marker for urinary tract infection brought on by E. Coli. (PMID: 25108210 ; PMID: 24909875 ). It has also been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000850 (Trimethylamine)

Trimethylamine Oxide.mol
  Mrv1652305271900312D          

  4  3  0  0  0  0            999 V2000
   -0.2062    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6187   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6187    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
M  END
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3D MOL for NP0000850 (Trimethylamine)

HMDB0000906
     RDKit          3D
Trimethylamine
 13 12  0  0  0  0  0  0  0  0999 V2000
   -0.8222   -1.0742    0.3410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0463   -0.0736   -0.3039 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5746    1.2525   -0.2362 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3656   -0.1719   -0.1145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7202   -0.7169    0.8642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1910   -1.8062   -0.4293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2423   -1.7034    1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1727    1.9418    0.2365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6521    1.6221   -1.2990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5680    1.3368    0.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6490   -1.2160    0.0869 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782    0.5078    0.6519 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8513    0.1012   -1.0875 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
  1  5  1  0
  1  6  1  0
  1  7  1  0
  3  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  4 13  1  0
M  END
Download

3D SDF for NP0000850 (Trimethylamine)

Trimethylamine Oxide.mol
  Mrv1652305271900312D          

  4  3  0  0  0  0            999 V2000
   -0.2062    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6187   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6187    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000850

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C3H9N/c1-4(2)3/h1-3H3

> <INCHI_KEY>
GETQZCLCWQTVFV-UHFFFAOYSA-N

> <FORMULA>
C3H9N

> <MOLECULAR_WEIGHT>
59.1103

> <EXACT_MASS>
59.073499293

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
7.638513658561092

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
trimethylamine

> <ALOGPS_LOGP>
-0.14

> <JCHEM_LOGP>
0.19016946566666637

> <ALOGPS_LOGS>
1.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.57376321286538

> <JCHEM_POLAR_SURFACE_AREA>
3.24

> <JCHEM_REFRACTIVITY>
19.9881

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.54e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
trimethylamine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0000850 (Trimethylamine)

HMDB0000906
     RDKit          3D
Trimethylamine
 13 12  0  0  0  0  0  0  0  0999 V2000
   -0.8222   -1.0742    0.3410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0463   -0.0736   -0.3039 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5746    1.2525   -0.2362 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3656   -0.1719   -0.1145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7202   -0.7169    0.8642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1910   -1.8062   -0.4293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2423   -1.7034    1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1727    1.9418    0.2365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6521    1.6221   -1.2990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5680    1.3368    0.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6490   -1.2160    0.0869 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782    0.5078    0.6519 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8513    0.1012   -1.0875 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
  1  5  1  0
  1  6  1  0
  1  7  1  0
  3  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  4 13  1  0
M  END
Download

PDB for NP0000850 (Trimethylamine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Trimethylamine Oxide.mol                          
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0      -0.385   0.000   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.155  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.155   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.155   0.000   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for NP0000850 (Trimethylamine)

COMPND    HMDB0000906
HETATM    1  C1  UNL     1      -0.822  -1.074   0.341  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.046  -0.074  -0.304  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.575   1.252  -0.236  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.366  -0.172  -0.114  1.00  0.00           C  
HETATM    5  H1  UNL     1      -1.720  -0.717   0.864  1.00  0.00           H  
HETATM    6  H2  UNL     1      -1.191  -1.806  -0.429  1.00  0.00           H  
HETATM    7  H3  UNL     1      -0.242  -1.703   1.069  1.00  0.00           H  
HETATM    8  H4  UNL     1       0.173   1.942   0.237  1.00  0.00           H  
HETATM    9  H5  UNL     1      -0.652   1.622  -1.299  1.00  0.00           H  
HETATM   10  H6  UNL     1      -1.568   1.337   0.221  1.00  0.00           H  
HETATM   11  H7  UNL     1       1.649  -1.216   0.087  1.00  0.00           H  
HETATM   12  H8  UNL     1       1.778   0.508   0.652  1.00  0.00           H  
HETATM   13  H9  UNL     1       1.851   0.101  -1.087  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    4
CONECT    3    8    9   10
CONECT    4   11   12   13
END
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SMILES for NP0000850 (Trimethylamine)

CN(C)C
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INCHI for NP0000850 (Trimethylamine)

InChI=1S/C3H9N/c1-4(2)3/h1-3H3
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View in JSmol
Synonyms
ValueSource
(CH3)3NChEBI
N(CH3)3ChEBI
N,N,N-TrimethylamineChEBI
N,N-DimethylmethanamineChEBI
NMe3ChEBI
TMAChEBI
TridimethylaminomethaneChEBI
TrimethylaminChEBI
DimethylmethaneamineHMDB
N,N-Dimethyl-methanamineHMDB
N-TrimethylamineHMDB
Trimethylamine anhydrousHMDB
Trimethylamine aqueous solutionHMDB
HI OF trimethylamineHMDB
HCL OF TrimethylamineHMDB
HBR OF TrimethylamineHMDB
Chemical FormulaC3H9N
Average Mass59.1103 Da
Monoisotopic Mass59.07350 Da
IUPAC Nametrimethylamine
Traditional Nametrimethylamine
CAS Registry Number75-50-3
SMILES
CN(C)C
InChI Identifier
InChI=1S/C3H9N/c1-4(2)3/h1-3H3
InChI KeyGETQZCLCWQTVFV-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, 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
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-07-29View Spectrum
Species
Species of Origin
Species NameSourceReference
Buthus martensi-
Coffea arabica L.FooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Coffea canephoraFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Ligusticum chuanxiungKNApSAcK Database
Oryza sativaFooDB
Theobroma cacaoFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Species Where Detected
Species NameSourceReference
Homo sapiens (Exhaled breath)KNApSAcK Database
Lobaria laetevirensKNApSAcK Database
Sticta fuliginosaKNApSAcK Database
Sticta sylvaticaKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as trialkylamines. These are organic compounds containing a trialkylamine group, characterized by exactly three alkyl groups bonded to the amino nitrogen.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentTrialkylamines
Alternative Parents
Substituents
  • Tertiary aliphatic amine
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point-117.1 °CNot Available
Boiling Point3.00 to 4.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility890 mg/mLNot Available
LogP0.16Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility654 g/LALOGPS
logP-0.14ALOGPS
logP0.19ChemAxon
logS1.04ALOGPS
pKa (Strongest Basic)9.57ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area3.24 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity19.99 m³·mol⁻¹ChemAxon
Polarizability7.64 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000906
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB011944
KNApSAcK IDC00001433
Chemspider ID1114
KEGG Compound IDC00565
BioCyc IDTRIMETHYLAMINE
BiGG IDNot Available
Wikipedia LinkTrimethylamine
METLIN ID3772
PubChem Compound1146
PDB IDNot Available
ChEBI ID18139
Good Scents IDrw1009301
References
General References
  1. Maschke S, Wahl A, Azaroual N, Boulet O, Crunelle V, Imbenotte M, Foulard M, Vermeersch G, Lhermitte M: 1H-NMR analysis of trimethylamine in urine for the diagnosis of fish-odour syndrome. Clin Chim Acta. 1997 Jul 25;263(2):139-46. [PubMed:9246418 ]
  2. Hillier SL: Diagnostic microbiology of bacterial vaginosis. Am J Obstet Gynecol. 1993 Aug;169(2 Pt 2):455-9. [PubMed:8357044 ]
  3. Chao CK, Zeisel SH: Formation of trimethylamine from dietary choline by Streptococcus sanguis I, which colonizes the mouth. J Nutr Biochem. 1990 Feb;1(2):89-97. [PubMed:15539190 ]
  4. Dzik-Jurasz AS, Prescot AP, Leach MO, Collins DJ: Non-invasive study of human gall bladder bile in vivo using (1)H-MR spectroscopy. Br J Radiol. 2003 Jul;76(907):483-6. [PubMed:12857709 ]
  5. Leys D, Basran J, Talfournier F, Chohan KK, Munro AW, Sutcliffe MJ, Scrutton NS: Flavin radicals, conformational sampling and robust design principles in interprotein electron transfer: the trimethylamine dehydrogenase-electron-transferring flavoprotein complex. Biochem Soc Symp. 2004;(71):1-14. [PubMed:15777008 ]
  6. Zeisel SH, daCosta KA, LaMont JT: Mono-, di- and trimethylamine in human gastric fluid: potential substrates for nitrosodimethylamine formation. Carcinogenesis. 1988 Jan;9(1):179-81. [PubMed:3335043 ]
  7. Mitchell SC, Zhang AQ, Barrett T, Ayesh R, Smith RL: Studies on the discontinuous N-oxidation of trimethylamine among Jordanian, Ecuadorian and New Guinean populations. Pharmacogenetics. 1997 Feb;7(1):45-50. [PubMed:9110361 ]
  8. Al-Waiz M, Ayesh R, Mitchell SC, Idle JR, Smith RL: A genetic polymorphism of the N-oxidation of trimethylamine in humans. Clin Pharmacol Ther. 1987 Nov;42(5):588-94. [PubMed:3677545 ]
  9. Kenyon S, Carmichael PL, Khalaque S, Panchal S, Waring R, Harris R, Smith RL, Mitchell SC: The passage of trimethylamine across rat and human skin. Food Chem Toxicol. 2004 Oct;42(10):1619-28. [PubMed:15304308 ]
  10. Thithapandha A: A pharmacogenetic study of trimethylaminuria in Orientals. Pharmacogenetics. 1997 Dec;7(6):497-501. [PubMed:9429235 ]
  11. Wang Z, Roberts AB, Buffa JA, Levison BS, Zhu W, Org E, Gu X, Huang Y, Zamanian-Daryoush M, Culley MK, DiDonato AJ, Fu X, Hazen JE, Krajcik D, DiDonato JA, Lusis AJ, Hazen SL: Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis. Cell. 2015 Dec 17;163(7):1585-95. doi: 10.1016/j.cell.2015.11.055. [PubMed:26687352 ]
  12. Lam CW, Law CY, Sze KH, To KK: Quantitative metabolomics of urine for rapid etiological diagnosis of urinary tract infection: evaluation of a microbial-mammalian co-metabolite as a diagnostic biomarker. Clin Chim Acta. 2015 Jan 1;438:24-8. doi: 10.1016/j.cca.2014.07.038. Epub 2014 Aug 6. [PubMed:25108210 ]
  13. Lam CW, Law CY, To KK, Cheung SK, Lee KC, Sze KH, Leung KF, Yuen KY: NMR-based metabolomic urinalysis: a rapid screening test for urinary tract infection. Clin Chim Acta. 2014 Sep 25;436:217-23. doi: 10.1016/j.cca.2014.05.014. Epub 2014 Jun 6. [PubMed:24909875 ]
  14. Rath S, Heidrich B, Pieper DH, Vital M: Uncovering the trimethylamine-producing bacteria of the human gut microbiota. Microbiome. 2017 May 15;5(1):54. doi: 10.1186/s40168-017-0271-9. [PubMed:28506279 ]
  15. Fennema D, Phillips IR, Shephard EA: Trimethylamine and Trimethylamine N-Oxide, a Flavin-Containing Monooxygenase 3 (FMO3)-Mediated Host-Microbiome Metabolic Axis Implicated in Health and Disease. Drug Metab Dispos. 2016 Nov;44(11):1839-1850. doi: 10.1124/dmd.116.070615. Epub 2016 May 17. [PubMed:27190056 ]