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Showing metabocard for Sarcosine (HMDB0000271)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:55:59 UTC
HMDB IDHMDB0000271
Secondary Accession Numbers
  • HMDB00271
Metabolite Identification
Common NameSarcosine
DescriptionSarcosine is the N-methyl derivative of glycine. Sarcosine is metabolized to glycine by the enzyme sarcosine dehydrogenase, while glycine-N-methyl transferase generates sarcosine from glycine. Sarcosine is a natural amino acid found in muscles and other body tissues. In the laboratory it may be synthesized from chloroacetic acid and methylamine. Sarcosine is naturally found in the metabolism of choline to glycine. Sarcosine is sweet to the taste and dissolves in water. It is used in manufacturing biodegradable surfactants and toothpastes as well as in other applications. Sarcosine is ubiquitous in biological materials and is present in such foods as egg yolks, turkey, ham, vegetables, legumes, etc. Sarcosine is formed from dietary intake of choline and from the metabolism of methionine, and is rapidly degraded to glycine. Sarcosine has no known toxicity, as evidenced by the lack of phenotypic manifestations of sarcosinemia, an inborn error of sarcosine metabolism. Sarcosinemia can result from severe folate deficiency because of the folate requirement for the conversion of sarcosine to glycine (Wikipedia ). Sarcosine has recently been identified as a biomarker for invasive prostate cancer. It was found to be greatly increased during prostate cancer progression to metastasis and could be detected in urine. Sarcosine levels were also increased in invasive prostate cancer cell lines relative to benign prostate epithelial cells (PMID: 19212411 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000271 (Sarcosine)

Sarcosine.mol
  Mrv1652305271900282D          

  6  5  0  0  0  0            999 V2000
    0.7145   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.2062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
M  END
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3D MOL for HMDB0000271 (Sarcosine)

HMDB0000271
     RDKit          3D
Sarcosine
 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.7383    0.0849    0.3796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8682   -0.1248   -0.7278 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4840    0.3122   -0.5419 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2161   -0.4956    0.4580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6716   -1.4506    1.0568 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5259   -0.1851    0.7313 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2503    0.5495    1.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1716   -0.8877    0.7558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5489    0.7824    0.0674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2084    0.1771   -1.6474 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0103    0.1301   -1.5239 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5803    1.4062   -0.3595 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2974   -0.2985    0.0933 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  2  0
  4  6  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  6 13  1  0
M  END
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3D SDF for HMDB0000271 (Sarcosine)

Sarcosine.mol
  Mrv1652305271900282D          

  6  5  0  0  0  0            999 V2000
    0.7145   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.2062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000271

> <DATABASE_NAME>
hmdb

> <SMILES>
CNCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H7NO2/c1-4-2-3(5)6/h4H,2H2,1H3,(H,5,6)

> <INCHI_KEY>
FSYKKLYZXJSNPZ-UHFFFAOYSA-N

> <FORMULA>
C3H7NO2

> <MOLECULAR_WEIGHT>
89.0932

> <EXACT_MASS>
89.047678473

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.659577131531222

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(methylamino)acetic acid

> <ALOGPS_LOGP>
-3.06

> <JCHEM_LOGP>
-3.1862609543807587

> <ALOGPS_LOGS>
0.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.056675239103723

> <JCHEM_PKA_STRONGEST_BASIC>
10.345946235601334

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
20.778

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.08e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sarcosine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000271 (Sarcosine)

HMDB0000271
     RDKit          3D
Sarcosine
 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.7383    0.0849    0.3796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8682   -0.1248   -0.7278 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4840    0.3122   -0.5419 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2161   -0.4956    0.4580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6716   -1.4506    1.0568 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5259   -0.1851    0.7313 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2503    0.5495    1.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1716   -0.8877    0.7558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5489    0.7824    0.0674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2084    0.1771   -1.6474 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0103    0.1301   -1.5239 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5803    1.4062   -0.3595 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2974   -0.2985    0.0933 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  2  0
  4  6  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  6 13  1  0
M  END
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PDB for HMDB0000271 (Sarcosine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Sarcosine.mol                                     
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       1.334  -0.385   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -1.334  -0.385   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       0.000  -1.155   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667  -1.155   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.334   1.155   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       2.667  -1.155   0.000  0.00  0.00           O+0
CONECT    1    3    5    6                                                  
CONECT    2    3    4                                                       
CONECT    3    2    1                                                       
CONECT    4    2                                                            
CONECT    5    1                                                            
CONECT    6    1                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0000271 (Sarcosine)

COMPND    HMDB0000271
HETATM    1  C1  UNL     1      -1.738   0.085   0.380  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.868  -0.125  -0.728  1.00  0.00           N  
HETATM    3  C2  UNL     1       0.484   0.312  -0.542  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.216  -0.496   0.458  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.672  -1.451   1.057  1.00  0.00           O  
HETATM    6  O2  UNL     1       2.526  -0.185   0.731  1.00  0.00           O  
HETATM    7  H1  UNL     1      -1.250   0.549   1.258  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.172  -0.888   0.756  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.549   0.782   0.067  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.208   0.177  -1.647  1.00  0.00           H  
HETATM   11  H5  UNL     1       1.010   0.130  -1.524  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.580   1.406  -0.359  1.00  0.00           H  
HETATM   13  H7  UNL     1       3.297  -0.299   0.093  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10
CONECT    3    4   11   12
CONECT    4    5    5    6
CONECT    6   13
END
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SMILES for HMDB0000271 (Sarcosine)

CNCC(O)=O
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INCHI for HMDB0000271 (Sarcosine)

InChI=1S/C3H7NO2/c1-4-2-3(5)6/h4H,2H2,1H3,(H,5,6)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC3H7NO2
Average Molecular Weight89.0932
Monoisotopic Molecular Weight89.047678473
IUPAC Name2-(methylamino)acetic acid
Traditional Namesarcosine
CAS Registry Number107-97-1
SMILES
CNCC(O)=O
InChI Identifier
InChI=1S/C3H7NO2/c1-4-2-3(5)6/h4H,2H2,1H3,(H,5,6)
InChI KeyFSYKKLYZXJSNPZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Amino acid
  • Carboxylic acid
  • Secondary aliphatic amine
  • Monocarboxylic acid or derivatives
  • Secondary amine
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point208 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility300 mg/mLNot Available
LogP-2.78HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Peroxisome
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Prostate
  • Skeletal Muscle
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Sarcosinemia
  1. Levy HL, Coulombe JT, Benjamin R: Massachusetts Metabolic Disorders Screening Program: III. Sarcosinemia. Pediatrics. 1984 Oct;74(4):509-13. [PubMed:6207480 ]
  2. Sewell AC, Krille M, Wilhelm I: Sarcosinaemia in a retarded, amaurotic child. Eur J Pediatr. 1986 Feb;144(5):508-10. [PubMed:2420598 ]
  3. Meissner T, Mayatepek E: Sarcosinaemia in a patient with severe progressive neurological damage and hypertrophic cardiomyopathy. J Inherit Metab Dis. 1997 Sep;20(5):717-8. [PubMed:9323574 ]
  4. Benarrosh A, Garnotel R, Henry A, Arndt C, Gillery P, Motte J, Bakchine S: A young adult with sarcosinemia. No benefit from long duration treatment with memantine. JIMD Rep. 2013;9:93-96. doi: 10.1007/8904_2012_185. Epub 2012 Oct 21. [PubMed:23430553 ]
  5. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
  6. Ronald Scott CC. (2014). In: Valle D, Beaudet AL, Vogelstein B, Kinzler KW, Antonarakis SE, Ballabio A, Gibson K, Mitchell G. eds. The Online Metabolic and Molecular Bases of Inherited Disease New York, NY. McGraw-Hill.
Colorectal cancer
  1. Ritchie SA, Ahiahonu PW, Jayasinghe D, Heath D, Liu J, Lu Y, Jin W, Kavianpour A, Yamazaki Y, Khan AM, Hossain M, Su-Myat KK, Wood PL, Krenitsky K, Takemasa I, Miyake M, Sekimoto M, Monden M, Matsubara H, Nomura F, Goodenowe DB: Reduced levels of hydroxylated, polyunsaturated ultra long-chain fatty acids in the serum of colorectal cancer patients: implications for early screening and detection. BMC Med. 2010 Feb 15;8:13. doi: 10.1186/1741-7015-8-13. [PubMed:20156336 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Stomach cancer
  1. Song H, Peng JS, Dong-Sheng Y, Yang ZL, Liu HL, Zeng YK, Shi XP, Lu BY: Serum metabolic profiling of human gastric cancer based on gas chromatography/mass spectrometry. Braz J Med Biol Res. 2012 Jan;45(1):78-85. Epub 2011 Nov 25. [PubMed:22124703 ]
Alzheimer's disease
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Frontotemporal dementia
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Lewy body disease
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Prostate cancer
  1. Soliman LC, Hui Y, Hewavitharana AK, Chen DD: Monitoring potential prostate cancer biomarkers in urine by capillary electrophoresis-tandem mass spectrometry. J Chromatogr A. 2012 Dec 7;1267:162-9. doi: 10.1016/j.chroma.2012.07.021. Epub 2012 Jul 14. [PubMed:22824219 ]
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 IDDB12519
Phenol Explorer Compound IDNot Available
FooDB IDFDB004048
KNApSAcK IDNot Available
Chemspider ID1057
KEGG Compound IDC00213
BioCyc IDSARCOSINE
BiGG ID34275
Wikipedia LinkSarcosine
METLIN ID51
PubChem Compound1088
PDB IDNot Available
ChEBI ID15611
Food Biomarker OntologyNot Available
VMH IDSARCS
MarkerDB IDMDB00000130
Good Scents IDNot Available
References
Synthesis ReferenceCipens, G.; Slavinska, V.; Sile, D.; Kreile, D.; Strautina, A.; Krikis, A.; Gutmanis, A. Synthesis of sarcosine and its use. Latvijas PSR Zinatnu Akademijas Vestis, Kimijas Serija (1986), (5), 515-24.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Peroxisomal sarcosine oxidase
General function:
Involved in oxidoreductase activity
Specific function:
Metabolizes sarcosine, L-pipecolic acid and L-proline.
Gene Name:
PIPOX
Uniprot ID:
Q9P0Z9
Molecular weight:
44065.515
Reactions
Sarcosine + Water + Oxygen → Glycine + Formaldehyde + Hydrogen peroxidedetails
Enzyme Details
2. Dimethylglycine dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
DMGDH
Uniprot ID:
Q9UI17
Molecular weight:
96810.135
Reactions
Dimethylglycine + electron-transfer flavoprotein + Water → Sarcosine + Formaldehyde + reduced electron-transfer flavoproteindetails
Dimethylglycine + Electron-transferring flavoprotein + Water → Sarcosine + Formaldehyde + Reduced electron-transferring flavoproteindetails
Enzyme Details
3. Glycine N-methyltransferase
General function:
Involved in folic acid binding
Specific function:
Catalyzes the methylation of glycine by using S-adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine.
Gene Name:
GNMT
Uniprot ID:
Q14749
Molecular weight:
32742.0
Reactions
S-Adenosylmethionine + Glycine → S-Adenosylhomocysteine + Sarcosinedetails
Enzyme Details
4. Sarcosine dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
SARDH
Uniprot ID:
Q9UL12
Molecular weight:
101035.985
Reactions
Sarcosine + Water + electron-transfer flavoprotein → Glycine + Formaldehyde + reduced electron-transfer flavoproteindetails
Sarcosine + Electron-transferring flavoprotein + Water → Glycine + Formaldehyde + Reduced electron-transferring flavoproteindetails
Enzyme Details
5. Proton-coupled amino acid transporter 2
General function:
Amino acid transport and metabolism
Specific function:
Involved in a pH-dependent electrogenic neuronal transport and sequestration of small amino acids amino acids such as glycine, alanine and proline. Inhibited by sarcosine
Gene Name:
SLC36A2
Uniprot ID:
Q495M3
Molecular weight:
53215.7