NP-MRD: Showing NP-Card for Isodomoic acid D (NP0341766)

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Record Information

Version

2.0

Created at

2024-09-12 10:46:00 UTC

Updated at

2024-09-12 10:46:00 UTC

NP-MRD ID

NP0341766

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Isodomoic acid D

Description

Not Available

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 43 43  0  0  0  0  0  0  0  0999 V2000
   -0.5382   -1.5886   -1.3385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0004   -0.8917   -0.0910 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2627   -0.5542   -0.1468 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0413    0.0871    0.8814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2970    0.4079    0.7401 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1964    0.2282   -0.3692 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0808   -0.8630   -1.3479 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6678    1.5357   -0.9429 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8844    1.6564   -2.1677 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8707    2.6256   -0.1207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8957   -0.4449    0.9439 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4579    1.0168    1.2950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6109    1.8988    1.0649 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2523    1.2162   -0.0722 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6337    1.6972   -0.2346 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2006    2.5001    0.5292 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4188    1.2455   -1.3265 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2907   -0.1353    0.6150 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2216   -1.0629    0.0058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3995   -2.3002    0.8366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3730   -2.8686    1.3372 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6966   -2.7735    1.0275 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0157   -0.8371   -1.9940 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2991   -2.0076   -1.9321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1366   -2.4598   -1.0745 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7551   -0.7686   -1.1304 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6741    0.2971    1.9060 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7768    0.9332    1.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2363   -0.0833    0.1800 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7080   -1.8345   -0.9715 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6363   -0.5765   -2.3434 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1448   -1.1837   -1.7114 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8282    3.0113   -0.1604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7909   -1.0180    1.8502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2304    1.1425    2.3403 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2700    1.4005    0.5607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3078    2.8212    0.6942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6535    1.2437   -0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1800    1.8121   -1.6860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7715    0.1227    1.6259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1676   -1.2724   -1.0697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2414   -0.5539    0.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1445   -2.8216    1.9445 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  5  1  0
  5  4  2  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 18  1  0
 18 19  1  0
 19 20  1  0
 20 22  1  0
 20 21  2  0
 14 15  1  0
 15 17  1  0
 15 16  2  0
  6  8  1  0
  8 10  1  0
  8  9  2  0
 18 11  1  0
  7 30  1  0
  7 31  1  0
  7 32  1  0
  6 29  1  1
  5 28  1  0
  4 27  1  0
  3 26  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
 11 34  1  1
 12 35  1  0
 12 36  1  0
 13 37  1  0
 14 38  1  6
 18 40  1  1
 19 41  1  0
 19 42  1  0
 22 43  1  0
 17 39  1  0
 10 33  1  0
M  END


  Mrv1652307301919592D          

 22 22  0  0  1  0            999 V2000
   -0.4318    0.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7334    3.3453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7854    2.7006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1266    2.2041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849    3.5194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6309   -0.3636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6937    1.4878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2271    1.3852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0745    3.8418    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1721    0.2590    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9865    1.0629    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8995   -1.1437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9940    0.1871    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1751    4.6606    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4189   -0.5201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3163    0.9465    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3582   -1.7663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7093   -1.3011    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9345    4.9830    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4838    5.1571    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2438   -0.5057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0189   -1.2416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  2  0  0  0  0
  8  1  1  0  0  0  0
  8  4  2  0  0  0  0
  9  2  1  1  0  0  0
  9  5  1  0  0  0  0
 10  6  1  1  0  0  0
 11  7  1  0  0  0  0
 11  8  1  1  0  0  0
 10 11  1  0  0  0  0
 12  6  1  0  0  0  0
 10 13  1  0  0  0  0
  9 14  1  0  0  0  0
 13 15  1  6  0  0  0
 16  7  1  0  0  0  0
 13 16  1  0  0  0  0
 17 12  2  0  0  0  0
 18 12  1  0  0  0  0
 19 14  2  0  0  0  0
 20 14  1  0  0  0  0
 21 15  2  0  0  0  0
 22 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0341766

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](\C=C/C=C(/C)[C@H]1CN[C@@H]([C@H]1CC(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/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+/m1/s1

> <INCHI_KEY>
VZFRNCSOCOPNDB-PQKHEMERSA-N

> <FORMULA>
C15H21NO6

> <MOLECULAR_WEIGHT>
311.334

> <EXACT_MASS>
311.1368874

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
31.325939558735826

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S)-4-[(2Z,4Z,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>
4.2155932749753955

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.682276677553546

> <JCHEM_PKA_STRONGEST_BASIC>
11.590344822229435

> <JCHEM_POLAR_SURFACE_AREA>
123.93000000000002

> <JCHEM_REFRACTIVITY>
79.03399999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-19         0                                  
HETATM    1  C   UNK     0      -0.806   1.659   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.369   6.245   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.466   5.041   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.236   4.114   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.278   6.570   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.178  -0.679   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.162   2.777   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.424   2.586   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.139   7.171   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.188   0.483   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.841   1.984   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.679  -2.135   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.722   0.349   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.327   8.700   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.515  -0.971   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       4.324   1.767   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       0.669  -3.297   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       3.191  -2.429   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.744   9.302   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.903   9.627   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.055  -0.944   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       3.769  -2.318   0.000  0.00  0.00           O+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3    4    5                                                       
CONECT    4    3    8                                                       
CONECT    5    3    9                                                       
CONECT    6   10   12                                                       
CONECT    7   11   16                                                       
CONECT    8    1    4   11                                                  
CONECT    9    2    5   14                                                  
CONECT   10    6   11   13                                                  
CONECT   11    7    8   10                                                  
CONECT   12    6   17   18                                                  
CONECT   13   10   15   16                                                  
CONECT   14    9   19   20                                                  
CONECT   15   13   21   22                                                  
CONECT   16    7   13                                                       
CONECT   17   12                                                            
CONECT   18   12                                                            
CONECT   19   14                                                            
CONECT   20   14                                                            
CONECT   21   15                                                            
CONECT   22   15                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol

Synonyms

Value	Source
Isodomoate D	Generator

Chemical Formula

C₁₅H₂₁NO₆

Average Mass

311.3340 Da

Monoisotopic Mass

311.13689 Da

IUPAC Name

(2S,3S,4S)-4-[(2Z,4Z,6R)-6-carboxy-6-methylhexa-2,4-dien-2-yl]-3-(carboxymethyl)pyrrolidine-2-carboxylic acid

Traditional Name

(2S,3S,4S)-4-[(2Z,4Z,6R)-6-carboxy-6-methylhexa-2,4-dien-2-yl]-3-(carboxymethyl)pyrrolidine-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

C[C@H](\C=C/C=C(/C)[C@H]1CN[C@@H]([C@H]1CC(O)=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/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+/m1/s1

InChI Key

VZFRNCSOCOPNDB-PQKHEMERSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Kainoids

Alternative Parents

Substituents

Kainoid skeleton
Proline or derivatives
Alpha-amino acid
Alpha-amino acid or derivatives
L-alpha-amino acid
Tricarboxylic acid or derivatives
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Pyrrolidine
Amino acid
Carboxylic acid
Secondary aliphatic amine
Azacycle
Organoheterocyclic compound
Secondary amine
Organonitrogen compound
Organic oxide
Organic nitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Amine
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.8	ChemAxon
pKa (Strongest Acidic)	1.68	ChemAxon
pKa (Strongest Basic)	11.59	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	123.93 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	79.03 m³·mol⁻¹	ChemAxon
Polarizability	31.33 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB017958

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6442551

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Isodomoic acid D (NP0341766)

MOL for NP0341766 (Isodomoic acid D)

3D MOL for NP0341766 (Isodomoic acid D)

3D SDF for NP0341766 (Isodomoic acid D)

3D-SDF for NP0341766 (Isodomoic acid D)

PDB for NP0341766 (Isodomoic acid D)

3D PDB for NP0341766 (Isodomoic acid D)

SMILES for NP0341766 (Isodomoic acid D)

INCHI for NP0341766 (Isodomoic acid D)

Structure for NP0341766 (Isodomoic acid D)

3D Structure for NP0341766 (Isodomoic acid D)