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Showing NP-Card for N-Carboxyglycine (NP0084243)

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Record Information
Version2.0
Created at2022-04-29 05:02:20 UTC
Updated at2022-04-29 05:02:20 UTC
NP-MRD IDNP0084243
Secondary Accession NumbersNone
Natural Product Identification
Common NameN-Carboxyglycine
DescriptionN-carboxyglycine belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. A glycine derivative in which one of the hydrogens attached to the amino group bas been replaced by a carboxy group. N-Carboxyglycine is found in Bergera koenegii, Citrus sinensis and Murraya paniculata . N-carboxyglycine is a weakly acidic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0084243 (N-Carboxyglycine)


  Mrv0541 09041212402D          

  8  7  0  0  0  0            999 V2000
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  2  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
M  END
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3D MOL for NP0084243 (N-Carboxyglycine)

     RDKit          3D

 13 12  0  0  0  0  0  0  0  0999 V2000
   -2.0687   -1.1898   -1.3999 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7537   -0.4929   -0.3859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6126    0.5235   -0.0580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5146   -0.7856    0.3550 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4729    0.2289   -0.0713 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8186    0.1909    0.2763 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4061   -0.6157    0.9742 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6430    1.2712   -0.1890 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6560    1.1067    0.7350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6391   -0.6054    1.4266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1335   -1.8131    0.1219 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0881    1.0073   -0.6442 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9498    1.1740   -1.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  8  1  0
  6  7  2  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  8 13  1  0
M  END
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3D SDF for NP0084243 (N-Carboxyglycine)


  Mrv0541 09041212402D          

  8  7  0  0  0  0            999 V2000
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  2  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084243

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CNC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H5NO4/c5-2(6)1-4-3(7)8/h4H,1H2,(H,5,6)(H,7,8)

> <INCHI_KEY>
UCWMWNHWCYYDTD-UHFFFAOYSA-N

> <FORMULA>
C3H5NO4

> <MOLECULAR_WEIGHT>
119.0761

> <EXACT_MASS>
119.021857653

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
9.573518318224043

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(carboxyamino)acetic acid

> <ALOGPS_LOGP>
-0.81

> <JCHEM_LOGP>
-0.8552318739999999

> <ALOGPS_LOGS>
-0.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.8921658250323508

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.04611086765943

> <JCHEM_POLAR_SURFACE_AREA>
86.63000000000001

> <JCHEM_REFRACTIVITY>
22.3017

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.69e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(carboxyamino)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0084243 (N-Carboxyglycine)

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PDB for NP0084243 (N-Carboxyglycine)
HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    5    6                                                  
CONECT    3    4    7    8                                                  
CONECT    4    1    3                                                       
CONECT    5    2                                                            
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    3                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0084243 (N-Carboxyglycine)
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SMILES for NP0084243 (N-Carboxyglycine)
OC(=O)CNC(O)=O
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INCHI for NP0084243 (N-Carboxyglycine)
InChI=1S/C3H5NO4/c5-2(6)1-4-3(7)8/h4H,1H2,(H,5,6)(H,7,8)
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View in JSmol
SynonymsNot Available
Chemical FormulaC3H5NO4
Average Mass119.0761 Da
Monoisotopic Mass119.02186 Da
IUPAC Name2-(carboxyamino)acetic acid
Traditional Name(carboxyamino)acetic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CNC(O)=O
InChI Identifier
InChI=1S/C3H5NO4/c5-2(6)1-4-3(7)8/h4H,1H2,(H,5,6)(H,7,8)
InChI KeyUCWMWNHWCYYDTD-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Bergera koenegii-
Citrus X sinensis (L.) Osbeck (pro. sp.)Plant
Murraya paniculataPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids and derivatives  
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
    • 

  • Carbonic acid derivative
    • 

  • Carbamic acid derivative
    • 

  • Carbamic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.81ALOGPS
logP-0.86ChemAxon
logS-0.32ALOGPS
pKa (Strongest Acidic)3.05ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.63 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.3 m³·mol⁻¹ChemAxon
Polarizability9.57 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9543263  
PDB IDNot Available
ChEBI ID87757  
Good Scents IDNot Available
References
General ReferencesNot Available