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Showing NP-Card for Sarcosine (NP0000314)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2022-05-31 21:10:28 UTC
NP-MRD IDNP0000314
Secondary Accession NumbersNone
Natural Product 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 NP0000314 (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
Download

3D MOL for NP0000314 (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
Download

3D SDF for NP0000314 (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>
NP0000314

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000314 (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
Download

PDB for NP0000314 (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 NP0000314 (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 NP0000314 (Sarcosine)

CNCC(O)=O
Download

INCHI for NP0000314 (Sarcosine)

InChI=1S/C3H7NO2/c1-4-2-3(5)6/h4H,2H2,1H3,(H,5,6)
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View in JSmol
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
Chemical FormulaC3H7NO2
Average Mass89.0932 Da
Monoisotopic Mass89.04768 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-05-31View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, experimental)Ahselim2022-05-31View Spectrum
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 IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)Varshavi.d262021-07-29View Spectrum
Species
Species of Origin
Species NameSourceReference
Astropecten irregularisLOTUS Database
Claviceps purpureaLOTUS Database
Homo sapiensLOTUS Database
Homo sapiens (Urine)Animalia
Juncus roemerianusLOTUS Database
Lates calcariferLOTUS Database
Mus musculusLOTUS Database
Sarcococca salignaLOTUS Database
Thalassiosira pseudonanaLOTUS Database
Triticum aestivumPlant
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point208 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility300 mg/mLNot Available
LogP-2.78Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility308 g/LALOGPS
logP-3.1ALOGPS
logP-3.2ChemAxon
logS0.54ALOGPS
pKa (Strongest Acidic)2.06ChemAxon
pKa (Strongest Basic)10.35ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity20.78 m³·mol⁻¹ChemAxon
Polarizability8.66 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000271
DrugBank IDDB12519
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021925
KNApSAcK IDC00052407
Chemspider ID1057
KEGG Compound IDC00213
BioCyc IDSARCOSINE
BiGG ID34275
Wikipedia LinkSarcosine
METLIN ID51
PubChem Compound1088
PDB IDNot Available
ChEBI ID15611
Good Scents IDrw1281741
References
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38. [PubMed:2026685 ]
  3. Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. [PubMed:14708889 ]
  4. Silwood CJ, Lynch E, Claxson AW, Grootveld MC: 1H and (13)C NMR spectroscopic analysis of human saliva. J Dent Res. 2002 Jun;81(6):422-7. [PubMed:12097436 ]
  5. Akare S, Martinez JD: Bile acid induces hydrophobicity-dependent membrane alterations. Biochim Biophys Acta. 2005 Jun 15;1735(1):59-67. [PubMed:15951237 ]
  6. Lim DS, Roberts R, Marian AJ: Expression profiling of cardiac genes in human hypertrophic cardiomyopathy: insight into the pathogenesis of phenotypes. J Am Coll Cardiol. 2001 Oct;38(4):1175-80. [PubMed:11583900 ]
  7. Bales JR, Sadler PJ, Nicholson JK, Timbrell JA: Urinary excretion of acetaminophen and its metabolites as studied by proton NMR spectroscopy. Clin Chem. 1984 Oct;30(10):1631-6. [PubMed:6206966 ]
  8. Heil M, Podebrad F, Prado E, Beck T, Mosand A, Sewell AC, Bohles H, Lehnert W: Enantioselective analysis of ketone bodies in patients with beta-ketothiolase deficiency, medium-chain acyl coenzyme A dehydrogenase deficiency and ketonemic vomiting. J Chromatogr B Biomed Sci Appl. 2000 Mar 10;739(2):313-24. [PubMed:10755375 ]
  9. Kang ES, Seyer J, Todd TA, Herrera C: Variability in the phenotypic expression of abnormal sarcosine metabolism in a family. Hum Genet. 1983;64(1):80-5. [PubMed:6192074 ]
  10. Vallera DA, Todhunter DA, Kuroki DW, Shu Y, Sicheneder A, Chen H: A bispecific recombinant immunotoxin, DT2219, targeting human CD19 and CD22 receptors in a mouse xenograft model of B-cell leukemia/lymphoma. Clin Cancer Res. 2005 May 15;11(10):3879-88. [PubMed:15897589 ]
  11. Hitomi J, Yamaguchi K, Kikuchi Y, Kimura T, Maruyama K, Nagasaki K: A novel calcium-binding protein in amniotic fluid, CAAF1: its molecular cloning and tissue distribution. J Cell Sci. 1996 Apr;109 ( Pt 4):805-15. [PubMed:8718672 ]
  12. Burton C, Gamagedara S, Ma Y: Partial enzymatic elimination and quantification of sarcosine from alanine using liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem. 2013 Apr;405(10):3153-8. doi: 10.1007/s00216-013-6740-5. Epub 2013 Jan 27. [PubMed:23354581 ]