NP-MRD: Showing NP-Card for {[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium (NP0171859)

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Record Information

Version

2.0

Created at

2022-09-03 08:33:12 UTC

Updated at

2022-09-03 08:33:12 UTC

NP-MRD ID

NP0171859

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium

Description

Dysibetaine belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. {[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium is found in Lamellodysidea herbacea. {[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium was first documented in 2004 (PMID: 15497982). Based on a literature review a significant number of articles have been published on Dysibetaine (PMID: 19173271) (PMID: 18318540) (PMID: 17997576) (PMID: 16408884) (PMID: 15136852) (PMID: 14961668).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 32  0  0  0  0  0  0  0  0999 V2000
   -1.3611   -1.0428   -1.3090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7733   -0.1724   -0.2447 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.9835    0.5072   -0.7660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2761   -0.9706    0.8626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8833    0.8391    0.1378 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5670    0.6260    0.1597 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1903    1.8893    0.6419 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0698    2.4468   -0.0292 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7558    2.4188    1.8616 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0837   -0.4546    1.0609 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5444   -0.4914    0.5659 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1431   -1.6855    0.8714 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2875   -0.3278   -0.9009 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0906   -0.7658   -1.9423 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1757    0.2999   -1.0900 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2550   -1.5030   -1.8298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8133   -1.9145   -0.8959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7841   -0.5728   -2.1005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6210    1.1600   -1.5973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3223    1.1988    0.0294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7404   -0.2174   -1.0788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5003   -0.3407    1.7477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6392   -1.7952    1.1617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2579   -1.3984    0.5169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1851    1.1842    1.1736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0591    1.7682   -0.4855 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4743    2.7471    2.5029 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7072   -1.4538    0.8929 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1123   -0.1537    2.1091 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408    0.4001    0.9540 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1227   -1.5645    0.7956 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0900   -0.6606   -1.8261 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  2  0
  6  7  1  1
  7  9  1  0
  7  8  2  0
 15  6  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  1
 12 31  1  0
 14 32  1  0
  9 27  1  0
M  CHG  1   2   1
M  END


  Mrv1652309032210332D          

 15 15  0  0  1  0            999 V2000
    2.7337    1.3843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9268    1.5559    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.0983    2.3628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7552    0.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7912    1.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2707    2.5120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   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
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  6  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
  6 15  1  0  0  0  0
M  CHG  1   2   1
M  END
> <DATABASE_ID>
NP0171859

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[N+](C)(C)C[C@]1(C[C@@H](O)C(O)=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N2O4/c1-11(2,3)5-9(8(14)15)4-6(12)7(13)10-9/h6,12H,4-5H2,1-3H3,(H-,10,13,14,15)/p+1/t6-,9-/m1/s1

> <INCHI_KEY>
YELMLJGVAMYPML-HZGVNTEJSA-O

> <FORMULA>
C9H17N2O4

> <MOLECULAR_WEIGHT>
217.244

> <EXACT_MASS>
217.118283456

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
21.51013826472367

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,4R)-2-carboxy-4,5-dihydroxy-3,4-dihydro-2H-pyrrol-2-yl]methyl}trimethylazanium

> <ALOGPS_LOGP>
-2.31

> <JCHEM_LOGP>
-5.081659664805079

> <ALOGPS_LOGS>
-2.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.903554496215378

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1447857848439145

> <JCHEM_PKA_STRONGEST_BASIC>
-2.041836562247521

> <JCHEM_POLAR_SURFACE_AREA>
90.12

> <JCHEM_REFRACTIVITY>
63.95550000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.10e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[(2R,4R)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium

> <JCHEM_VEBER_RULE>
0

$$$$

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       5.103   2.584   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.597   2.904   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       3.917   4.411   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.276   1.398   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.090   3.224   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.029   3.224   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.477   2.904   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.505   4.689   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7   10   15                                             
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    6   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    6                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₇N₂O₄

Average Mass

217.2440 Da

Monoisotopic Mass

217.11828 Da

IUPAC Name

{[(2R,4R)-2-carboxy-4,5-dihydroxy-3,4-dihydro-2H-pyrrol-2-yl]methyl}trimethylazanium

Traditional Name

{[(2R,4R)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium

CAS Registry Number

Not Available

SMILES

C[N+](C)(C)C[C@]1(C[C@@H](O)C(O)=N1)C(O)=O

InChI Identifier

InChI=1S/C9H16N2O4/c1-11(2,3)5-9(8(14)15)4-6(12)7(13)10-9/h6,12H,4-5H2,1-3H3,(H-,10,13,14,15)/p+1/t6-,9-/m1/s1

InChI Key

YELMLJGVAMYPML-HZGVNTEJSA-O

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

Species Name	Source	Reference
Lamellodysidea herbacea	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Oxoproline
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Pyrrolidone
2-pyrrolidone
Tetraalkylammonium salt
Pyrrolidine
Quaternary ammonium salt
Carboxamide group
Lactam
Secondary carboxylic acid amide
Secondary alcohol
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Amine
Organic cation
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	-2.3	ALOGPS
logP	-5.1	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	3.14	ChemAxon
pKa (Strongest Basic)	-2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	90.12 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	63.96 m³·mol⁻¹	ChemAxon
Polarizability	21.51 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

Not Available

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

21589615

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Isaacson J, Kobayashi Y: An Ugi reaction in the total synthesis of (-)-dysibetaine. Angew Chem Int Ed Engl. 2009;48(10):1845-8. doi: 10.1002/anie.200805709. [PubMed:19173271 ]
Isaacson J, Loo M, Kobayashi Y: Total synthesis of (+/-)-dysibetaine. Org Lett. 2008 Apr 3;10(7):1461-3. doi: 10.1021/ol800245m. Epub 2008 Mar 5. [PubMed:18318540 ]
Siddiquee TA, Lukesh JM, Lindeman S, Donaldson WA: Synthesis of cyclopropanes via organoiron methodology: preparation of rac-dysibetaine CPa. J Org Chem. 2007 Dec 7;72(25):9802-3. doi: 10.1021/jo7020604. Epub 2007 Nov 13. [PubMed:17997576 ]
Ijzendoorn DR, Botman PN, Blaauw RH: Diastereoselective cationic tandem cyclizations to N-heterocyclic scaffolds: total synthesis of (-)-dysibetaine PP. Org Lett. 2006 Jan 19;8(2):239-42. doi: 10.1021/ol052598r. [PubMed:16408884 ]
Langlois N, Le Nguyen BK: Diastereoselective syntheses of deoxydysibetaine, dysibetaine, and its 4-epimer. J Org Chem. 2004 Oct 29;69(22):7558-64. doi: 10.1021/jo040216+. [PubMed:15497982 ]
Wardrop DJ, Burge MS: Total synthesis of (-)-dysibetaine via a nitrenium ion cyclization-dienone cleavage strategy. Chem Commun (Camb). 2004 May 21;(10):1230-1. doi: 10.1039/b403081h. Epub 2004 Apr 27. [PubMed:15136852 ]
Sakai R, Suzuki K, Shimamoto K, Kamiya H: Novel betaines from a micronesian sponge Dysidea herbacea. J Org Chem. 2004 Feb 20;69(4):1180-5. doi: 10.1021/jo0355045. [PubMed:14961668 ]
LOTUS database [Link]

Showing NP-Card for {[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium (NP0171859)

MOL for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

3D MOL for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

3D SDF for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

3D-SDF for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

PDB for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

3D PDB for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

SMILES for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

INCHI for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

Structure for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)

3D Structure for NP0171859 ({[(2r,4r)-2-carboxy-4,5-dihydroxy-3,4-dihydropyrrol-2-yl]methyl}trimethylazanium)