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Showing NP-Card for Isodomoic acid E (NP0341765)

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Record Information
Version2.0
Created at2024-09-12 10:45:44 UTC
Updated at2024-09-12 10:45:44 UTC
NP-MRD IDNP0341765
Secondary Accession NumbersNone
Natural Product Identification
Common NameIsodomoic acid E
DescriptionIsodomoic acid E is also known as isodomoate e. Isodomoic acid E was first documented in 2011 (PMID: 21350768). Based on a literature review very few articles have been published on Isodomoic acid E.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0341765 (Isodomoic acid E)


  Mrv2104 05272313172D          

 22 22  0  0  0  0            999 V2000
    0.1218   -0.2755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4611    1.3868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0035    1.5150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7537    0.2548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6962    1.0778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2650   -1.0880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5542    0.0552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8633   -0.7097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9914    0.7548    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3670   -1.6183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0403   -1.3701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6803   -0.8245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3554   -1.3598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0466    2.3388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7571    1.1794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4716    1.5919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2253    1.2564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9172    1.7057    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6091    1.2564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9172    2.5307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3235    1.6689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6523    0.4325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  4  1  0  0  0  0
  8  7  1  0  0  0  0
  9  2  1  0  0  0  0
  9  7  1  0  0  0  0
 10  6  2  0  0  0  0
 11  6  1  0  0  0  0
 12  8  2  0  0  0  0
 13  8  1  0  0  0  0
  3 14  1  0  0  0  0
  3 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  6  0  0  0
 19 21  2  0  0  0  0
 19 22  1  0  0  0  0
M  END
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3D MOL for NP0341765 (Isodomoic acid E)

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3D SDF for NP0341765 (Isodomoic acid E)

  Mrv2104 05272313172D          

 22 22  0  0  0  0            999 V2000
    0.1218   -0.2755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4611    1.3868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0035    1.5150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7537    0.2548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6962    1.0778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2650   -1.0880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5542    0.0552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8633   -0.7097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9914    0.7548    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3670   -1.6183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0403   -1.3701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6803   -0.8245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3554   -1.3598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0466    2.3388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7571    1.1794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4716    1.5919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2253    1.2564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9172    1.7057    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6091    1.2564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9172    2.5307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3235    1.6689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6523    0.4325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  4  1  0  0  0  0
  8  7  1  0  0  0  0
  9  2  1  0  0  0  0
  9  7  1  0  0  0  0
 10  6  2  0  0  0  0
 11  6  1  0  0  0  0
 12  8  2  0  0  0  0
 13  8  1  0  0  0  0
  3 14  1  0  0  0  0
  3 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  6  0  0  0
 19 21  2  0  0  0  0
 19 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0341765

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](\C=C\C=C(/C)C1CNC(C1CC(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/b5-3+,8-4+/t9-,10?,11?,13?/s2

> <INCHI_KEY>
VZFRNCSOCOPNDB-IVCHIYERNA-N

> <FORMULA>
C15H21NO6

> <MOLECULAR_WEIGHT>
311.334

> <EXACT_MASS>
311.1368874

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
31.314608303710514

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(2E,4E,6R)-6-carboxy-6-methylhexa-2,4-dien-2-yl]-3-(carboxymethyl)pyrrolidine-2-carboxylic acid

> <JCHEM_LOGP>
-1.7909643388701357

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.215593274975397

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.682276677553546

> <JCHEM_PKA_STRONGEST_BASIC>
11.590344822229437

> <JCHEM_POLAR_SURFACE_AREA>
123.93000000000002

> <JCHEM_REFRACTIVITY>
79.03399999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-[(2E,4E,6R)-6-carboxy-6-methylhexa-2,4-dien-2-yl]-3-(carboxymethyl)pyrrolidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0341765 (Isodomoic acid E)
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PDB for NP0341765 (Isodomoic acid E)
HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0       0.227  -0.514   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.727   2.589   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.007   2.828   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.407   0.476   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.300   2.012   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.495  -2.031   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.901   0.103   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.478  -1.325   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.717   1.409   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -0.685  -3.021   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.942  -2.558   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.003  -1.539   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.530  -2.538   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.087   4.366   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.413   2.202   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.747   2.972   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.154   2.345   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.445   3.184   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.737   2.345   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.445   4.724   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -8.071   3.115   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -6.818   0.807   0.000  0.00  0.00           O+0
CONECT    1    4    6                                                       
CONECT    2    5    9                                                       
CONECT    3    5   14   15                                                  
CONECT    4    1    5    7                                                  
CONECT    5    2    3    4                                                  
CONECT    6    1   10   11                                                  
CONECT    7    4    8    9                                                  
CONECT    8    7   12   13                                                  
CONECT    9    2    7                                                       
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    8                                                            
CONECT   13    8                                                            
CONECT   14    3                                                            
CONECT   15    3   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18   21   22                                                  
CONECT   20   18                                                            
CONECT   21   19                                                            
CONECT   22   19                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

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3D PDB for NP0341765 (Isodomoic acid E)
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SMILES for NP0341765 (Isodomoic acid E)
C[C@H](\C=C\C=C(/C)C1CNC(C1CC(O)=O)C(O)=O)C(O)=O
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INCHI for NP0341765 (Isodomoic acid E)
InChI=1/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/b5-3+,8-4+/t9-,10?,11?,13?/s2
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Synonyms
ValueSource
Isodomoate eGenerator
Chemical FormulaC15H21NO6
Average Mass311.3340 Da
Monoisotopic Mass311.13689 Da
IUPAC Name4-[(2E,4E,6R)-6-carboxy-6-methylhexa-2,4-dien-2-yl]-3-(carboxymethyl)pyrrolidine-2-carboxylic acid
Traditional Name4-[(2E,4E,6R)-6-carboxy-6-methylhexa-2,4-dien-2-yl]-3-(carboxymethyl)pyrrolidine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
C[C@H](\C=C\C=C(/C)C1CNC(C1CC(O)=O)C(O)=O)C(O)=O
InChI Identifier
InChI=1/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/b5-3+,8-4+/t9-,10?,11?,13?/s2
InChI KeyVZFRNCSOCOPNDB-IVCHIYERNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as kainoids. These are non-proteigenous amino acids with a structure characterized by the presence of a pyrrolidine ring bearing two dicarboxylic acid groups.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentKainoids  
Alternative Parents
Substituents
  • Kainoid skeleton
    • 

  • Proline or derivatives
    • 

  • Alpha-amino acid or derivatives
    • 

  • Tricarboxylic acid or derivatives
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Pyrrolidine carboxylic acid
    • 

  • Pyrrolidine
    • 

  • Amino acid
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Secondary amine
    • 

  • Secondary aliphatic amine
    • 

  • Carboxylic acid
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-1.8ChemAxon
pKa (Strongest Acidic)1.68ChemAxon
pKa (Strongest Basic)11.59ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area123.93 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity79.03 m³·mol⁻¹ChemAxon
Polarizability31.31 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Lemiere G, Sedehizadeh S, Toueg J, Fleary-Roberts N, Clayden J: A general synthetic approach to the amnesic shellfish toxins: total synthesis of (-)-isodomoic acid B, (-)-isodomoic acid E and (-)-isodomoic acid F. Chem Commun (Camb). 2011 Apr 7;47(13):3745-7. doi: 10.1039/c1cc00048a. Epub 2011  Feb 24. [PubMed:21350768  ]