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Showing metabocard for Trimethylamine (HMDB0000906)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:17 UTC
HMDB IDHMDB0000906
Secondary Accession Numbers
  • HMDB00906
Metabolite Identification
Common NameTrimethylamine
Description
Structure
Data?1676999717
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000906 (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
Download

3D MOL for HMDB0000906 (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 HMDB0000906 (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>
HMDB0000906

> <DATABASE_NAME>
hmdb

> <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 HMDB0000906 (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 HMDB0000906 (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 HMDB0000906 (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 HMDB0000906 (Trimethylamine)

CN(C)C
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INCHI for HMDB0000906 (Trimethylamine)

InChI=1S/C3H9N/c1-4(2)3/h1-3H3
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View in JSmolView NMR AssignmentsView Stereo Labels
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 Molecular Weight59.1103
Monoisotopic Molecular Weight59.073499293
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
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
Ontology
Physiological effect
Health effectOrganoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Environmental roleIndustrial applicationBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-117.1 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility890 mg/mLNot Available
LogP0.16HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Epidermis
  • Skeletal Muscle
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Kidney disease
  1. Bain MA, Faull R, Milne RW, Evans AM: Oral L-carnitine: metabolite formation and hemodialysis. Curr Drug Metab. 2006 Oct;7(7):811-6. [PubMed:17073580 ]
Uremia
  1. Duranton F, Cohen G, De Smet R, Rodriguez M, Jankowski J, Vanholder R, Argiles A: Normal and pathologic concentrations of uremic toxins. J Am Soc Nephrol. 2012 Jul;23(7):1258-70. doi: 10.1681/ASN.2011121175. Epub 2012 May 24. [PubMed:22626821 ]
Early preeclampsia
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: Metabolomics and first-trimester prediction of early-onset preeclampsia. J Matern Fetal Neonatal Med. 2012 Oct;25(10):1840-7. doi: 10.3109/14767058.2012.680254. Epub 2012 Apr 28. [PubMed:22494326 ]
Pregnancy
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: Metabolomics and first-trimester prediction of early-onset preeclampsia. J Matern Fetal Neonatal Med. 2012 Oct;25(10):1840-7. doi: 10.3109/14767058.2012.680254. Epub 2012 Apr 28. [PubMed:22494326 ]
  2. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol. 2013 Jan;208(1):58.e1-7. doi: 10.1016/j.ajog.2012.11.003. Epub 2012 Nov 13. [PubMed:23159745 ]
Late-onset preeclampsia
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol. 2013 Jan;208(1):58.e1-7. doi: 10.1016/j.ajog.2012.11.003. Epub 2012 Nov 13. [PubMed:23159745 ]
Crohn's disease
  1. Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y: Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 2007 Feb;6(2):546-51. [PubMed:17269711 ]
Ulcerative colitis
  1. Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y: Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 2007 Feb;6(2):546-51. [PubMed:17269711 ]
  2. Le Gall G, Noor SO, Ridgway K, Scovell L, Jamieson C, Johnson IT, Colquhoun IJ, Kemsley EK, Narbad A: Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res. 2011 Sep 2;10(9):4208-18. doi: 10.1021/pr2003598. Epub 2011 Aug 8. [PubMed:21761941 ]
Irritable bowel syndrome
  1. Le Gall G, Noor SO, Ridgway K, Scovell L, Jamieson C, Johnson IT, Colquhoun IJ, Kemsley EK, Narbad A: Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res. 2011 Sep 2;10(9):4208-18. doi: 10.1021/pr2003598. Epub 2011 Aug 8. [PubMed:21761941 ]
Diverticular disease
  1. Tursi A, Mastromarino P, Capobianco D, Elisei W, Miccheli A, Capuani G, Tomassini A, Campagna G, Picchio M, Giorgetti G, Fabiocchi F, Brandimarte G: Assessment of Fecal Microbiota and Fecal Metabolome in Symptomatic Uncomplicated Diverticular Disease of the Colon. J Clin Gastroenterol. 2016 Oct;50 Suppl 1:S9-S12. doi: 10.1097/MCG.0000000000000626. [PubMed:27622378 ]
Perillyl alcohol administration for cancer treatment
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Pancreatic cancer
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Periodontal disease
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Trimethylaminuria
  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. Chalmers RA, Bain MD, Michelakakis H, Zschocke J, Iles RA: Diagnosis and management of trimethylaminuria (FMO3 deficiency) in children. J Inherit Metab Dis. 2006 Feb;29(1):162-72. [PubMed:16601883 ]
  3. Treacy E, Johnson D, Pitt JJ, Danks DM: Trimethylaminuria, fish odour syndrome: a new method of detection and response to treatment with metronidazole. J Inherit Metab Dis. 1995;18(3):306-12. [PubMed:7474897 ]
  4. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Dimethylglycine Dehydrogenase Deficiency
  1. Moolenaar SH, Poggi-Bach J, Engelke UF, Corstiaensen JM, Heerschap A, de Jong JG, Binzak BA, Vockley J, Wevers RA: Defect in dimethylglycine dehydrogenase, a new inborn error of metabolism: NMR spectroscopy study. Clin Chem. 1999 Apr;45(4):459-64. [PubMed:10102904 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB011944
KNApSAcK IDC00001433
Chemspider ID1114
KEGG Compound IDC00565
BioCyc IDTRIMETHYLAMINE
BiGG IDNot Available
Wikipedia LinkTrimethylamine
METLIN ID3772
PubChem Compound1146
PDB IDNot Available
ChEBI ID18139
Food Biomarker OntologyNot Available
VMH IDM03053
MarkerDB IDMDB00000280
Good Scents IDNot Available
References
Synthesis ReferenceHirohata, Saneo; Tanba, Kiyonobu; Inoue, Kenichi. Preparation of trimethylamine by zeolite-catalyzed reaction of methanol and ammonia. Jpn. Kokai Tokkyo Koho (2006), 5pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References

Enzymes

Enzyme Details
1. Dimethylaniline monooxygenase [N-oxide-forming] 5
General function:
Involved in flavin-containing monooxygenase activity
Specific function:
In contrast with other forms of FMO it does not seem to be a drug-metabolizing enzyme.
Gene Name:
FMO5
Uniprot ID:
P49326
Molecular weight:
32480.04
Reactions
Trimethylamine + NADPH + Hydrogen Ion + Oxygen → Trimethylamine N-oxide + NADP + Waterdetails
Enzyme Details
2. Dimethylaniline monooxygenase [N-oxide-forming] 2
General function:
Involved in flavin-containing monooxygenase activity
Specific function:
Catalyzes the N-oxidation of certain primary alkylamines to their oximes via an N-hydroxylamine intermediate. Inactive toward certain tertiary amines, such as imipramine or chloropromazine. Can catalyze the S-oxidation of methimazole. The truncated form is catalytically inactive.
Gene Name:
FMO2
Uniprot ID:
Q99518
Molecular weight:
53643.29
Reactions
Trimethylamine + NADPH + Hydrogen Ion + Oxygen → Trimethylamine N-oxide + NADP + Waterdetails
Enzyme Details
3. Dimethylaniline monooxygenase [N-oxide-forming] 4
General function:
Involved in flavin-containing monooxygenase activity
Specific function:
This protein is involved in the oxidative metabolism of a variety of xenobiotics such as drugs and pesticides.
Gene Name:
FMO4
Uniprot ID:
P31512
Molecular weight:
63342.055
Reactions
Trimethylamine + NADPH + Hydrogen Ion + Oxygen → Trimethylamine N-oxide + NADP + Waterdetails
Enzyme Details
4. Dimethylaniline monooxygenase [N-oxide-forming] 3
General function:
Involved in flavin-containing monooxygenase activity
Specific function:
Involved in the oxidative metabolism of a variety of xenobiotics such as drugs and pesticides. It N-oxygenates primary aliphatic alkylamines as well as secondary and tertiary amines. Plays an important role in the metabolism of trimethylamine (TMA), via the production of TMA N-oxide (TMAO). Is also able to perform S-oxidation when acting on sulfide compounds.
Gene Name:
FMO3
Uniprot ID:
P31513
Molecular weight:
60032.975
Reactions
Trimethylamine + NADPH + Oxygen → Trimethylamine N-oxide + NADP + Waterdetails
Trimethylamine + NADPH + Hydrogen Ion + Oxygen → Trimethylamine N-oxide + NADP + Waterdetails
Enzyme Details
5. Dimethylaniline monooxygenase [N-oxide-forming] 1
General function:
Involved in flavin-containing monooxygenase activity
Specific function:
This protein is involved in the oxidative metabolism of a variety of xenobiotics such as drugs and pesticides. Form I catalyzes the N-oxygenation of secondary and tertiary amines.
Gene Name:
FMO1
Uniprot ID:
Q01740
Molecular weight:
60310.285
Reactions
Trimethylamine + NADPH + Hydrogen Ion + Oxygen → Trimethylamine N-oxide + NADP + Waterdetails