Showing metabocard for Trimethylamine (MMDBc0000168)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:38:22 UTC
Update Date2024-09-29 06:39:10 UTC
Metabolite IDMMDBc0000168
Metabolite 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 (Wikipedia ). 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 (Wikipedia ). 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 (Wikipedia ). 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 ">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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f46bb038758>

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 #<Metabolite:0x00007f46bb038758>

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 #<Metabolite:0x00007f46bb038758>

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>
MMDBc0000168

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f46bb038758>

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 #<Metabolite:0x00007f46bb038758>

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
Download

3D PDB for #<Metabolite:0x00007f46bb038758>

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
Download

SMILES for #<Metabolite:0x00007f46bb038758>

CN(C)C
Download

INCHI for #<Metabolite:0x00007f46bb038758>

InChI=1S/C3H9N/c1-4(2)3/h1-3H3
Download
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
Molecular FormulaC3H9N
Average Mass59.1103
Monoisotopic Mass59.073499293
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