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Showing NP-Card for amino(2-methylidenecyclopropyl)acetic acid (NP0213360)

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Record Information
Version2.0
Created at2022-09-05 12:19:28 UTC
Updated at2022-09-05 12:19:28 UTC
NP-MRD IDNP0213360
Secondary Accession NumbersNone
Natural Product Identification
Common Nameamino(2-methylidenecyclopropyl)acetic acid
Description2-Amino-2-(2-methylidenecyclopropyl)acetic acid 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). amino(2-methylidenecyclopropyl)acetic acid is found in Litchi chinensis. 2-Amino-2-(2-methylidenecyclopropyl)acetic acid is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0213360 (amino(2-methylidenecyclopropyl)acetic acid)


  Mrv1533004241500152D          

  9  9  0  0  0  0            999 V2000
   -0.4763    2.1263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8888   -0.2382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.1263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.9513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6671    1.7138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
Download

3D MOL for NP0213360 (amino(2-methylidenecyclopropyl)acetic acid)

     RDKit          3D

 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5556   -0.7146   -0.6015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5390   -0.3318    0.1514 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9844    0.8884    0.9171 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2749   -0.3727    0.9061 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9707   -0.5482    0.0618 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6482   -0.3252   -1.3513 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0232    0.4043    0.4711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4516    0.3851    1.6549 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5552    1.3249   -0.4202 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5494   -1.7360   -0.9563 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3849   -0.0855   -0.8853 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6302    1.1237    1.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7330    1.7425    0.2428 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2331   -0.9493    1.8753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3565   -1.5939    0.1184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5603   -0.2795   -1.8778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1599   -1.2007   -1.6650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1590    2.2686   -0.4365 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  3
  5  7  1  0
  7  9  1  0
  7  8  2  0
  2  4  1  0
  6 16  1  0
  6 17  1  0
  5 15  1  6
  4 14  1  1
  3 12  1  0
  3 13  1  0
  1 10  1  0
  1 11  1  0
  9 18  1  0
M  END
Download

3D SDF for NP0213360 (amino(2-methylidenecyclopropyl)acetic acid)


  Mrv1533004241500152D          

  9  9  0  0  0  0            999 V2000
   -0.4763    2.1263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8888   -0.2382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.1263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.9513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6671    1.7138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0213360

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(C1CC1=C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO2/c1-3-2-4(3)5(7)6(8)9/h4-5H,1-2,7H2,(H,8,9)

> <INCHI_KEY>
MPIZVHPMGFWKMJ-UHFFFAOYSA-N

> <FORMULA>
C6H9NO2

> <MOLECULAR_WEIGHT>
127.143

> <EXACT_MASS>
127.063328534

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.751699292201659

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-2-(2-methylidenecyclopropyl)acetic acid

> <ALOGPS_LOGP>
-2.56

> <JCHEM_LOGP>
-2.4777971771743

> <ALOGPS_LOGS>
0.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4131130100560396

> <JCHEM_PKA_STRONGEST_BASIC>
9.51877689483445

> <JCHEM_POLAR_SURFACE_AREA>
63.32000000000001

> <JCHEM_REFRACTIVITY>
32.0168

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.08e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
amino(2-methylidenecyclopropyl)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0213360 (amino(2-methylidenecyclopropyl)acetic acid)

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PDB for NP0213360 (amino(2-methylidenecyclopropyl)acetic acid)
HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  N   UNK     0      -0.889   3.969   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.445   3.199   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.215   0.325   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.325   0.325   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.659  -0.445   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.778   3.969   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.778   5.509   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       3.112   3.199   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3    5                                                       
CONECT    5    4    3    6                                                  
CONECT    6    5                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0213360 (amino(2-methylidenecyclopropyl)acetic acid)
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SMILES for NP0213360 (amino(2-methylidenecyclopropyl)acetic acid)
NC(C1CC1=C)C(O)=O
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INCHI for NP0213360 (amino(2-methylidenecyclopropyl)acetic acid)
InChI=1S/C6H9NO2/c1-3-2-4(3)5(7)6(8)9/h4-5H,1-2,7H2,(H,8,9)
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View in JSmol
Synonyms
ValueSource
2-Amino-2-(2-methylidenecyclopropyl)acetateGenerator
Chemical FormulaC6H9NO2
Average Mass127.1430 Da
Monoisotopic Mass127.06333 Da
IUPAC Name2-amino-2-(2-methylidenecyclopropyl)acetic acid
Traditional Nameamino(2-methylidenecyclopropyl)acetic acid
CAS Registry NumberNot Available
SMILES
NC(C1CC1=C)C(O)=O
InChI Identifier
InChI=1S/C6H9NO2/c1-3-2-4(3)5(7)6(8)9/h4-5H,1-2,7H2,(H,8,9)
InChI KeyMPIZVHPMGFWKMJ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Litchi chinensisLOTUS 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
    • 

  • Amino acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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-2.6ALOGPS
logP-2.5ChemAxon
logS0.21ALOGPS
pKa (Strongest Acidic)2.41ChemAxon
pKa (Strongest Basic)9.52ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity32.02 m³·mol⁻¹ChemAxon
Polarizability12.75 ųChemAxon
Number of Rings1ChemAxon
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 IDC00001381  
Chemspider IDNot Available
KEGG Compound IDC08292  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound25203707  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]