Showing metabocard for Glycine (MMDBc0000034)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:27:57 UTC
Update Date2022-08-30 23:11:37 UTC
Metabolite IDMMDBc0000034
Metabolite Identification
Common NameGlycine
DescriptionGlycine is a simple, nonessential amino acid, although experimental animals show reduced growth on low-glycine diets. The average adult ingests 3 to 5 grams of glycine daily. Glycine is involved in the body's production of DNA, phospholipids, and collagen, and in the release of energy. Glycine levels are effectively measured in plasma in both normal patients and those with inborn errors of glycine metabolism (http://www.dcnutrition.com/AminoAcids/). Nonketotic hyperglycinaemia (OMIM: 606899 ) is an autosomal recessive condition caused by deficient enzyme activity of the glycine cleavage enzyme system (EC 2.1.1.10). The glycine cleavage enzyme system comprises four proteins: P-, T-, H- and L-proteins (EC 1.4.4.2, EC 2.1.2.10, and EC 1.8.1.4 for P-, T-, and L-proteins). Mutations have been described in the GLDC (OMIM: 238300 ), AMT (OMIM: 238310 ), and GCSH (OMIM: 238330 ) genes encoding the P-, T-, and H-proteins respectively. The glycine cleavage system catalyzes the oxidative conversion of glycine into carbon dioxide and ammonia, with the remaining one-carbon unit transferred to folate as methylenetetrahydrofolate. It is the main catabolic pathway for glycine and it also contributes to one-carbon metabolism. Patients with a deficiency of this enzyme system have increased glycine in plasma, urine, and cerebrospinal fluid (CSF) with an increased CSF:plasma glycine ratio (PMID: 16151895 ). Glycine is also found to be associated with carbamoyl phosphate synthetase deficiency, iminoglycinuria, maple syrup urine disease, phenylketonuria, propionic acidemia, sarcosinemia, and tyrosinemia I, which are inborn errors of metabolism.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055d24afd9518>


  Mrv1652309272007262D          

  5  4  0  0  0  0            999 V2000
    1.8187    0.2250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1042   -0.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5331   -0.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8187    1.0500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3897    0.2250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  2  0  0  0  0
  3  1  1  0  0  0  0
  2  5  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x000055d24afd9518>

HMDB0000123
     RDKit          3D
Glycine
 10  9  0  0  0  0  0  0  0  0999 V2000
   -1.3016    0.3297   -0.2404 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4493   -0.7254    0.2495 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9473   -0.3534   -0.0120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9359   -1.0679    0.2981 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2069    0.8562   -0.6381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0181    0.6315   -1.1938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3525    1.1349    0.4174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5656   -0.7983    1.3646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7374   -1.7090   -0.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3344    1.7017   -0.0731 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  5 10  1  0
M  END
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3D SDF for #<Metabolite:0x000055d24afd9518>


  Mrv1652309272007262D          

  5  4  0  0  0  0            999 V2000
    1.8187    0.2250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1042   -0.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5331   -0.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8187    1.0500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3897    0.2250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  2  0  0  0  0
  3  1  1  0  0  0  0
  2  5  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000034

> <DATABASE_NAME>
MIME

> <SMILES>
NCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)

> <INCHI_KEY>
DHMQDGOQFOQNFH-UHFFFAOYSA-N

> <FORMULA>
C2H5NO2

> <MOLECULAR_WEIGHT>
75.0666

> <EXACT_MASS>
75.032028409

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
6.647019971293048

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-aminoacetic acid

> <ALOGPS_LOGP>
-3.34

> <JCHEM_LOGP>
-3.409459573132419

> <ALOGPS_LOGS>
0.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.3074568824727444

> <JCHEM_PKA_STRONGEST_BASIC>
9.240341660583645

> <JCHEM_POLAR_SURFACE_AREA>
63.31999999999999

> <JCHEM_REFRACTIVITY>
16.0034

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.52e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x000055d24afd9518>

HMDB0000123
     RDKit          3D
Glycine
 10  9  0  0  0  0  0  0  0  0999 V2000
   -1.3016    0.3297   -0.2404 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4493   -0.7254    0.2495 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9473   -0.3534   -0.0120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9359   -1.0679    0.2981 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2069    0.8562   -0.6381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0181    0.6315   -1.1938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3525    1.1349    0.4174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5656   -0.7983    1.3646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7374   -1.7090   -0.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3344    1.7017   -0.0731 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  5 10  1  0
M  END
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PDB for #<Metabolite:0x000055d24afd9518>

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0       3.395   0.420   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.061  -0.350   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.728  -0.350   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.395   1.960   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       0.727   0.420   0.000  0.00  0.00           N+0
CONECT    1    2    4    3                                                  
CONECT    2    1    5                                                       
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    2                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for #<Metabolite:0x000055d24afd9518>

COMPND    HMDB0000123
HETATM    1  N1  UNL     1      -1.302   0.330  -0.240  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.449  -0.725   0.249  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.947  -0.353  -0.012  1.00  0.00           C  
HETATM    4  O1  UNL     1       1.936  -1.068   0.298  1.00  0.00           O  
HETATM    5  O2  UNL     1       1.207   0.856  -0.638  1.00  0.00           O  
HETATM    6  H1  UNL     1      -1.018   0.631  -1.194  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.352   1.135   0.417  1.00  0.00           H  
HETATM    8  H3  UNL     1      -0.566  -0.798   1.365  1.00  0.00           H  
HETATM    9  H4  UNL     1      -0.737  -1.709  -0.172  1.00  0.00           H  
HETATM   10  H5  UNL     1       1.334   1.702  -0.073  1.00  0.00           H  
CONECT    1    2    6    7
CONECT    2    3    8    9
CONECT    3    4    4    5
CONECT    5   10
END
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SMILES for #<Metabolite:0x000055d24afd9518>

NCC(O)=O
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INCHI for #<Metabolite:0x000055d24afd9518>

InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
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Synonyms
ValueSource
Aminoacetic acidChEBI
AminoessigsaeureChEBI
Aminoethanoic acidChEBI
GChEBI
GlyChEBI
GlycinChEBI
GlycocollChEBI
GlykokollChEBI
GlyzinChEBI
H2N-CH2-COOHChEBI
HglyChEBI
LeimzuckerChEBI
AminoacetateGenerator
AminoethanoateGenerator
2-AminoacetateHMDB
2-Aminoacetic acidHMDB
AciportHMDB
Amino-acetateHMDB
Amino-acetic acidHMDB
GlicoaminHMDB
GlycolixirHMDB
GlycostheneHMDB
Gyn-hydralinHMDB
PadilHMDB
Glycine carbonate (1:1), monosodium saltHMDB
Glycine carbonate (2:1), monopotassium saltHMDB
Glycine sulfate (3:1)HMDB
Glycine, monoammonium saltHMDB
Glycine, monosodium saltHMDB
Glycine, sodium hydrogen carbonateHMDB
Monoammonium salt glycineHMDB
Calcium salt glycineHMDB
Glycine hydrochloride (2:1)HMDB
Glycine phosphate (1:1)HMDB
Glycine, monopotasssium saltHMDB
Monopotasssium salt glycineHMDB
Monosodium salt glycineHMDB
Glycine carbonate (2:1), monolithium saltHMDB
Glycine carbonate (2:1), monosodium saltHMDB
Glycine hydrochlorideHMDB
Glycine, copper saltHMDB
Hydrochloride, glycineHMDB
Salt glycine, monoammoniumHMDB
Acid, aminoaceticHMDB
Cobalt salt glycineHMDB
Copper salt glycineHMDB
Glycine phosphateHMDB
Glycine, calcium saltHMDB
Glycine, calcium salt (2:1)HMDB
Glycine, cobalt saltHMDB
Phosphate, glycineHMDB
Salt glycine, monosodiumHMDB
Molecular FormulaC2H5NO2
Average Mass75.0666
Monoisotopic Mass75.032028409
IUPAC Name2-aminoacetic acid
Traditional Nameglycine
CAS Registry Number56-40-6
SMILES
NCC(O)=O
InChI Identifier
InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
InChI KeyDHMQDGOQFOQNFH-UHFFFAOYSA-N