Showing metabocard for Sarcosine (MMDBc0000778)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:54:44 UTC
Update Date2024-10-10 00:37:28 UTC
Metabolite IDMMDBc0000778
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9235b1e5d0>

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 #<Metabolite:0x00007f9235b1e5d0>

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 #<Metabolite:0x00007f9235b1e5d0>

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>
MMDBc0000778

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f9235b1e5d0>

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 #<Metabolite:0x00007f9235b1e5d0>

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 #<Metabolite:0x00007f9235b1e5d0>

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 #<Metabolite:0x00007f9235b1e5d0>

CNCC(O)=O
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INCHI for #<Metabolite:0x00007f9235b1e5d0>

InChI=1S/C3H7NO2/c1-4-2-3(5)6/h4H,2H2,1H3,(H,5,6)
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Synonyms
ValueSource
(Methylamino)acetic acidChEBI
(Methylamino)ethanoic acidChEBI
L-SarcosineChEBI
MeGlyChEBI
Methylaminoacetic acidChEBI
N-Methylaminoacetic acidChEBI
N-MethylglycineChEBI
SarChEBI
Sarcosinic acidChEBI
(Methylamino)acetateGenerator
(Methylamino)ethanoateGenerator
MethylaminoacetateGenerator
N-MethylaminoacetateGenerator
SarcosinateGenerator
(Methylamino)-acetateHMDB
(Methylamino)-acetic acidHMDB
MethylglycineHMDB
N-Methyl-glycineHMDB
SarcosinHMDB
Sodium sarcosinateHMDB
Magnesium sarcosylateHMDB
Sarcosinate, sodiumHMDB
Sarcosine hydrochlorideHMDB
Sarcosylate, magnesiumHMDB
N MethylglycineHMDB
Sarcosine monosodium saltHMDB
Molecular FormulaC3H7NO2
Average Mass89.0932
Monoisotopic Mass89.047678473
IUPAC Name2-(methylamino)acetic acid
Traditional Namesarcosine
CAS Registry NumberNot Available
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