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Showing NP-Card for (2s)-2-amino-3-methylidenepentanoic acid (NP0167242)

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Record Information
Version2.0
Created at2022-09-03 02:47:15 UTC
Updated at2022-09-03 02:47:15 UTC
NP-MRD IDNP0167242
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s)-2-amino-3-methylidenepentanoic acid
Description3-Methylenenorvaline 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. (2s)-2-amino-3-methylidenepentanoic acid is found in Philadelphus coronarius. Based on a literature review very few articles have been published on 3-methylenenorvaline.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0167242 ((2s)-2-amino-3-methylidenepentanoic acid)


  Mrv1652309032204472D          

  9  8  0  0  1  0            999 V2000
    1.2375   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  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 NP0167242 ((2s)-2-amino-3-methylidenepentanoic acid)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    0.7200   -0.5276   -1.6925 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2810   -0.2517   -0.4726 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0152    0.6826    0.4234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2494    1.1721   -0.3111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9895   -0.9265   -0.0317 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5211   -1.7344   -1.1045 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9883    0.1206    0.2779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0514    0.1971   -0.3836 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7987    1.0569    1.3035 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1851   -1.2005   -2.3289 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6451   -0.0671   -2.0709 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3155    0.1102    1.3092 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4041    1.5230    0.7534 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0265    1.7349   -1.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8441    1.8427    0.3635 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9339    0.3360   -0.5537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7949   -1.5790    0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5337   -1.9135   -1.0194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9543   -2.5904   -1.2763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9878    2.0146    1.0567 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0
  3  2  1  0
  2  1  2  3
  2  5  1  0
  5  6  1  0
  5  7  1  0
  7  9  1  0
  7  8  2  0
  4 14  1  0
  4 15  1  0
  4 16  1  0
  3 12  1  0
  3 13  1  0
  1 10  1  0
  1 11  1  0
  5 17  1  1
  6 18  1  0
  6 19  1  0
  9 20  1  0
M  END
Download

3D SDF for NP0167242 ((2s)-2-amino-3-methylidenepentanoic acid)


  Mrv1652309032204472D          

  9  8  0  0  1  0            999 V2000
    1.2375   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0167242

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(=C)[C@H](N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO2/c1-3-4(2)5(7)6(8)9/h5H,2-3,7H2,1H3,(H,8,9)/t5-/m0/s1

> <INCHI_KEY>
SBTLHKXSISNXTP-YFKPBYRVSA-N

> <FORMULA>
C6H11NO2

> <MOLECULAR_WEIGHT>
129.159

> <EXACT_MASS>
129.078978598

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.396107084041073

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-3-methylidenepentanoic acid

> <ALOGPS_LOGP>
-1.99

> <JCHEM_LOGP>
-1.776344277325989

> <ALOGPS_LOGS>
-0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.6306944488283963

> <JCHEM_PKA_STRONGEST_BASIC>
9.002303458021947

> <JCHEM_POLAR_SURFACE_AREA>
63.32000000000001

> <JCHEM_REFRACTIVITY>
33.7944

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-3-methylidenepentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0167242 ((2s)-2-amino-3-methylidenepentanoic acid)

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PDB for NP0167242 ((2s)-2-amino-3-methylidenepentanoic acid)
HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       2.310  -0.206   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0167242 ((2s)-2-amino-3-methylidenepentanoic acid)
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SMILES for NP0167242 ((2s)-2-amino-3-methylidenepentanoic acid)
CCC(=C)[C@H](N)C(O)=O
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INCHI for NP0167242 ((2s)-2-amino-3-methylidenepentanoic acid)
InChI=1S/C6H11NO2/c1-3-4(2)5(7)6(8)9/h5H,2-3,7H2,1H3,(H,8,9)/t5-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H11NO2
Average Mass129.1590 Da
Monoisotopic Mass129.07898 Da
IUPAC Name(2S)-2-amino-3-methylidenepentanoic acid
Traditional Name(2S)-2-amino-3-methylidenepentanoic acid
CAS Registry NumberNot Available
SMILES
CCC(=C)[C@H](N)C(O)=O
InChI Identifier
InChI=1S/C6H11NO2/c1-3-4(2)5(7)6(8)9/h5H,2-3,7H2,1H3,(H,8,9)/t5-/m0/s1
InChI KeySBTLHKXSISNXTP-YFKPBYRVSA-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
Philadelphus coronariusLOTUS Database
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
    • 

  • Branched fatty acid
    • 

  • Methyl-branched fatty acid
    • 

  • Unsaturated fatty acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • 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-2ALOGPS
logP-1.8ChemAxon
logS-0.1ALOGPS
pKa (Strongest Acidic)2.63ChemAxon
pKa (Strongest Basic)9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity33.79 m³·mol⁻¹ChemAxon
Polarizability13.4 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 ID32972951  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound18635633  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]