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Showing NP-Card for alpha-(Methylenecyclopropyl)glycine (NP0050682)

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Record Information
Version2.0
Created at2022-04-27 22:01:53 UTC
Updated at2022-04-27 22:01:53 UTC
NP-MRD IDNP0050682
Secondary Accession NumbersNone
Natural Product Identification
Common Namealpha-(Methylenecyclopropyl)glycine
Description(S)-2-Amino-2-[(S)-2-methylenecyclopropyl]acetic acid belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. alpha-(Methylenecyclopropyl)glycine is found in Acer pseudoplatanus , Billia hippocastanum and Litchi sinensis. Based on a literature review very few articles have been published on (S)-2-Amino-2-[(S)-2-methylenecyclopropyl]acetic acid.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0050682 (alpha-(Methylenecyclopropyl)glycine)


  Mrv1652304282200012D          

  9  9  0  0  1  0            999 V2000
    0.2382    1.7138    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4763    2.1263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.9513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1908    1.7138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.1263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  2  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
    1.3651   -0.2382    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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  1  0  0  0
  6  1  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
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3D MOL for NP0050682 (alpha-(Methylenecyclopropyl)glycine)

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3D SDF for NP0050682 (alpha-(Methylenecyclopropyl)glycine)

  Mrv1652304282200012D          

  9  9  0  0  1  0            999 V2000
    0.2382    1.7138    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4763    2.1263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.9513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1908    1.7138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.1263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  2  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
    1.3651   -0.2382    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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  1  0  0  0
  6  1  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050682

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H]([C@H]1CC1=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)/t4-,5-/m0/s1

> <INCHI_KEY>
MPIZVHPMGFWKMJ-WHFBIAKZSA-N

> <FORMULA>
C6H9NO2

> <MOLECULAR_WEIGHT>
127.143

> <EXACT_MASS>
127.063328534

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.676925864383094

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-2-[(1S)-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>
63.31999999999999

> <JCHEM_REFRACTIVITY>
32.0168

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.08e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylenecyclopropylglycine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0050682 (alpha-(Methylenecyclopropyl)glycine)
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PDB for NP0050682 (alpha-(Methylenecyclopropyl)glycine)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       0.445   3.199   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.889   3.969   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.889   5.509   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -2.223   3.199   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       1.778   3.969   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.215   0.325   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.548  -0.445   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.325   0.325   0.000  0.00  0.00           C+0
CONECT    1    2    5    6                                                  
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1                                                            
CONECT    6    1    7    9                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    6                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0050682 (alpha-(Methylenecyclopropyl)glycine)
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SMILES for NP0050682 (alpha-(Methylenecyclopropyl)glycine)
N[C@@H]([C@H]1CC1=C)C(O)=O
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INCHI for NP0050682 (alpha-(Methylenecyclopropyl)glycine)
InChI=1S/C6H9NO2/c1-3-2-4(3)5(7)6(8)9/h4-5H,1-2,7H2,(H,8,9)/t4-,5-/m0/s1
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Synonyms
ValueSource
(S)-2-Amino-2-[(S)-2-methylenecyclopropyl]acetateGenerator
Chemical FormulaC6H9NO2
Average Mass127.1430 Da
Monoisotopic Mass127.06333 Da
IUPAC Name(2S)-2-amino-2-[(1S)-2-methylidenecyclopropyl]acetic acid
Traditional Namemethylenecyclopropylglycine
CAS Registry NumberNot Available
SMILES
N[C@@H]([C@H]1CC1=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)/t4-,5-/m0/s1
InChI KeyMPIZVHPMGFWKMJ-WHFBIAKZSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Acer pseudoplatanusPlant
Billia hippocastanumPlant
Litchi sinensisPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentL-alpha-amino acids  
Alternative Parents
Substituents
  • L-alpha-amino acid
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Amine
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
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
Polarizability12.68 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 IDNot Available
Chemspider ID390185  
KEGG Compound IDC08292  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound441452  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available