Np mrd loader

Showing NP-Card for Dimethylglycine (NP0000814)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:42:26 UTC
NP-MRD IDNP0000814
Secondary Accession NumbersNone
Natural Product Identification
Common NameDimethylglycine
DescriptionDimethylglycine (DMG) is an amino acid derivative found in the cells of all plants and animals and can be obtained in the diet in small amounts from grains and meat. The human body produces DMG when metabolizing choline into Glycine. Dimethylglycine that is not metabolized in the liver is transported by the circulatory system to body tissue. Dimethylglycine was popular with Russian athletes and cosmonauts owing to its reputed ability to increase endurance and reduce fatigue. DMG is also a byproduct of homocysteine metabolism. Homocysteine and betaine are converted to methionine and N, N-dimethylglycine by betaine-homocysteine methyltransferase. Dimethylglycine in the urine is a biomarker for the consumption of legumes.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000814 (Dimethylglycine)


  Mrv1652306051920022D          

  7  6  0  0  0  0            999 V2000
   -1.6069   -1.1598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8924   -0.7473    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1780   -1.1598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8924    0.0776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3214   -0.7473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3214    0.0776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0358   -1.1598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  END
Download

3D MOL for NP0000814 (Dimethylglycine)

HMDB0000092
     RDKit          3D
Dimethylglycine
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.7842    0.6357   -0.2009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6350    0.0011    0.4783 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7991   -1.4137    0.1222 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5245    0.5872   -0.1366 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8142    0.2420    0.5151 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9399   -0.5887    1.4294 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9400    0.9123    0.0530 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6848    0.0041   -0.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4880    0.7445   -1.2570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9388    1.6661    0.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7054   -1.7686    0.6912 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0811   -2.0087    0.3459 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0968   -1.4503   -0.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5575    0.2699   -1.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4360    1.6896   -0.1581 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8389    0.4776   -0.1164 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
  4  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  7 16  1  0
M  END
Download

3D SDF for NP0000814 (Dimethylglycine)


  Mrv1652306051920022D          

  7  6  0  0  0  0            999 V2000
   -1.6069   -1.1598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8924   -0.7473    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1780   -1.1598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8924    0.0776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3214   -0.7473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3214    0.0776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0358   -1.1598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000814

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN(C)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO2/c1-5(2)3-4(6)7/h3H2,1-2H3,(H,6,7)

> <INCHI_KEY>
FFDGPVCHZBVARC-UHFFFAOYSA-N

> <FORMULA>
C4H9NO2

> <MOLECULAR_WEIGHT>
103.1198

> <EXACT_MASS>
103.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
10.470047738620533

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(dimethylamino)acetic acid

> <ALOGPS_LOGP>
-1.70

> <JCHEM_LOGP>
-3.0607825071662678

> <ALOGPS_LOGS>
0.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8808127451470078

> <JCHEM_PKA_STRONGEST_BASIC>
9.691600277978429

> <JCHEM_POLAR_SURFACE_AREA>
40.54

> <JCHEM_REFRACTIVITY>
26.0727

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dimethylglycine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000814 (Dimethylglycine)

HMDB0000092
     RDKit          3D
Dimethylglycine
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.7842    0.6357   -0.2009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6350    0.0011    0.4783 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7991   -1.4137    0.1222 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5245    0.5872   -0.1366 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8142    0.2420    0.5151 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9399   -0.5887    1.4294 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9400    0.9123    0.0530 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6848    0.0041   -0.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4880    0.7445   -1.2570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9388    1.6661    0.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7054   -1.7686    0.6912 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0811   -2.0087    0.3459 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0968   -1.4503   -0.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5575    0.2699   -1.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4360    1.6896   -0.1581 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8389    0.4776   -0.1164 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
  4  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  7 16  1  0
M  END
Download

PDB for NP0000814 (Dimethylglycine)

HEADER    PROTEIN                                 05-JUN-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-19         0                                  
HETATM    1  C   UNK     0      -3.000  -2.165   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -1.666  -1.395   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -0.332  -2.165   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.666   0.145   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.333  -1.395   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.333   0.145   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -5.667  -2.165   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for NP0000814 (Dimethylglycine)

COMPND    HMDB0000092
HETATM    1  C1  UNL     1      -1.784   0.636  -0.201  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.635   0.001   0.478  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.799  -1.414   0.122  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.524   0.587  -0.137  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.814   0.242   0.515  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.940  -0.589   1.429  1.00  0.00           O  
HETATM    7  O2  UNL     1       2.940   0.912   0.053  1.00  0.00           O  
HETATM    8  H1  UNL     1      -2.685   0.004  -0.157  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.488   0.745  -1.257  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.939   1.666   0.187  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.705  -1.769   0.691  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.081  -2.009   0.346  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.097  -1.450  -0.940  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.558   0.270  -1.230  1.00  0.00           H  
HETATM   15  H8  UNL     1       0.436   1.690  -0.158  1.00  0.00           H  
HETATM   16  H9  UNL     1       3.839   0.478  -0.116  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    4
CONECT    3   11   12   13
CONECT    4    5   14   15
CONECT    5    6    6    7
CONECT    7   16
END
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SMILES for NP0000814 (Dimethylglycine)

CN(C)CC(O)=O
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INCHI for NP0000814 (Dimethylglycine)

InChI=1S/C4H9NO2/c1-5(2)3-4(6)7/h3H2,1-2H3,(H,6,7)
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View in JSmol
Synonyms
ValueSource
(Dimethylamino)acetic acidChEBI
2-(Dimethylamino)acetic acidChEBI
N,N-Dimethylaminoacetic acidChEBI
N-MethylsarcosineChEBI
(Dimethylamino)acetateGenerator
2-(Dimethylamino)acetateGenerator
N,N-DimethylaminoacetateGenerator
N,N-DimethylglycineHMDB
N-Methylsarcosine N,N-dimethyl-glycineHMDB
Dimethylglycine, monopotassium saltHMDB
Dimethylglycine, sodium saltHMDB
Dimethylglycine, calcium saltHMDB
Dimethylglycine monohydrochlorideHMDB
2-(N,N-Dimethylamino)acetic acidHMDB
DMGHMDB
DimethylglycineHMDB
Chemical FormulaC4H9NO2
Average Mass103.1198 Da
Monoisotopic Mass103.06333 Da
IUPAC Name2-(dimethylamino)acetic acid
Traditional Namedimethylglycine
CAS Registry Number1118-68-9
SMILES
CN(C)CC(O)=O
InChI Identifier
InChI=1S/C4H9NO2/c1-5(2)3-4(6)7/h3H2,1-2H3,(H,6,7)
InChI KeyFFDGPVCHZBVARC-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 400 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.d262021-08-02View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
Lates calcariferLOTUS Database
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
Paris polyphyllaLOTUS Database
PhasianidaeFooDB
Phasianus colchicusFooDB
Pseudostellaria heterophyllaLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Thalassiosira pseudonanaLOTUS Database
Trypanosoma bruceiLOTUS Database
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
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
  • Tertiary amine
  • Tertiary aliphatic amine
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point185.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-2.91Tsai, R. S., Testa, B., El Tayar, N., & Carrupt, P. A. (1991). Structure-lipophilicity relationships of zwitterionic amino acids. Journal of the Chemical Society, Perkin Transactions 2, (11), 1797-1802.
Predicted Properties
PropertyValueSource
Water Solubility939 g/LALOGPS
logP-1.7ALOGPS
logP-3.1ChemAxon
logS0.96ALOGPS
pKa (Strongest Acidic)1.88ChemAxon
pKa (Strongest Basic)9.69ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area40.54 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity26.07 m³·mol⁻¹ChemAxon
Polarizability10.47 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000092
DrugBank IDDB02083
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021893
KNApSAcK IDC00052266
Chemspider ID653
KEGG Compound IDC01026
BioCyc IDDIMETHYL-GLYCINE
BiGG ID36652
Wikipedia LinkDimethylglycine
METLIN ID277
PubChem Compound673
PDB IDNot Available
ChEBI ID17724
Good Scents IDNot Available
References
General References
  1. Binzak BA, Vockley JG, Jenkins RB, Vockley J: Structure and analysis of the human dimethylglycine dehydrogenase gene. Mol Genet Metab. 2000 Mar;69(3):181-7. [PubMed:10767172 ]
  2. Binzak BA, Wevers RA, Moolenaar SH, Lee YM, Hwu WL, Poggi-Bach J, Engelke UF, Hoard HM, Vockley JG, Vockley J: Cloning of dimethylglycine dehydrogenase and a new human inborn error of metabolism, dimethylglycine dehydrogenase deficiency. Am J Hum Genet. 2001 Apr;68(4):839-47. Epub 2001 Feb 28. [PubMed:11231903 ]
  3. 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 ]
  4. Laryea MD, Steinhagen F, Pawliczek S, Wendel U: Simple method for the routine determination of betaine and N,N-dimethylglycine in blood and urine. Clin Chem. 1998 Sep;44(9):1937-41. [PubMed:9732980 ]
  5. McGregor DO, Dellow WJ, Lever M, George PM, Robson RA, Chambers ST: Dimethylglycine accumulates in uremia and predicts elevated plasma homocysteine concentrations. Kidney Int. 2001 Jun;59(6):2267-72. [PubMed:11380830 ]
  6. Look MP, Riezler R, Reichel C, Brensing KA, Rockstroh JK, Stabler SP, Spengler U, Berthold HK, Sauerbruch T: Is the increase in serum cystathionine levels in patients with liver cirrhosis a consequence of impaired homocysteine transsulfuration at the level of gamma-cystathionase? Scand J Gastroenterol. 2000 Aug;35(8):866-72. [PubMed:10994627 ]
  7. Cicek G, Vuorinen T, Stahle I, Stepanek P, Freudenberg N, Brandsch R: Coxsackievirus B3 infection induces anti-flavoprotein antibodies in mice. Clin Exp Immunol. 2000 Dec;122(3):404-9. [PubMed:11122247 ]
  8. Lever M, George PM, Dellow WJ, Scott RS, Chambers ST: Homocysteine, glycine betaine, and N,N-dimethylglycine in patients attending a lipid clinic. Metabolism. 2005 Jan;54(1):1-14. [PubMed:15562374 ]
  9. Xia JH, Yu KP, Liu CY, Pan Q, Zheng D, Dai HP: [Molecular clonging of the human dimethyglycine dehydrogenase-like gene (DMGDHL1) from the sarcosinemia critical region at 9q34]. Yi Chuan Xue Bao. 1999;26(6):591-7. [PubMed:10876657 ]
  10. Jansen M, Hansen TA: Non-growth-associated demethylation of dimethylsulfoniopropionate by (homo)acetogenic bacteria. Appl Environ Microbiol. 2001 Jan;67(1):300-6. [PubMed:11133459 ]