NP-MRD: Showing NP-Card for (3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol (NP0235144)

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Record Information

Version

2.0

Created at

2022-09-06 17:36:31 UTC

Updated at

2022-09-06 17:36:31 UTC

NP-MRD ID

NP0235144

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol

Description

Decarbamoylsaxitoxin, also known as DCSTX-saxitoxin, belongs to the class of organic compounds known as saxitoxins, gonyautoxins, and derivatives. Saxitoxins, gonyautoxins, and derivatives are compounds with a structure based on a 2,6-diamino-4-methyl-pyrrolo[1,2-c]purin-10-ol skeleton. Decarbamoylsaxitoxin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. (3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol is found in Apis cerana. (3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol was first documented in 2003 (PMID: 12740803). Based on a literature review a small amount of articles have been published on decarbamoylsaxitoxin (PMID: 12924931) (PMID: 15019474) (PMID: 15146927) (PMID: 16192070).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 36  0  0  0  0  0  0  0  0999 V2000
   -0.2073    4.0065    1.6882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5326    3.0528    1.9573 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2366    2.0404    1.1770 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5019    2.0789   -0.0394 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5396    0.7298   -0.6173 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7840   -0.0072   -0.1510 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0461    0.7209   -0.5039 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1118   -0.0145    0.0116 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7201   -1.3439   -0.6892 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5587   -2.0948   -0.3561 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5700   -3.3862   -0.4310 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4483   -3.8504   -0.7399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5846   -1.3561    0.0524 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8803   -1.8017    0.5192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8076   -0.7717   -0.0755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9534    0.3791   -0.5626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9211    0.4811   -1.9319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4483    1.5543    0.0034 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6229    0.0738    0.0601 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5853    0.6748    1.3677 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9557    2.9083   -0.4790 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4453    0.7304   -1.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7273   -0.0857    0.9546 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0359    1.6901    0.0095 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2078    0.7886   -1.5949 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8953   -0.3388    0.9230 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4852   -1.7232   -1.2835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8813   -1.8090    1.6163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1079   -2.8347    0.1862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3535   -1.2556   -0.9029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4909   -0.4418    0.7440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6389   -0.3836   -2.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0120    1.3408    0.7718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7686    0.2483    2.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  9  1  0
  9 10  1  0
 10 11  2  0
 10 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  1
 20  3  1  0
  3  2  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
 19 13  1  0
  5 19  1  0
  8 26  1  0
  7 24  1  0
  7 25  1  0
  6 23  1  1
  9 27  1  0
 11 12  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
 15 31  1  0
 17 32  1  0
 18 33  1  0
 20 34  1  0
  2  1  1  0
  4 21  1  0
  5 22  1  6
M  END


  Mrv1652309062219362D          

 18 20  0  0  1  0            999 V2000
   -0.1712   -0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    0.9521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.3646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4663   -2.3299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6458   -2.4162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3102   -1.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5958   -2.0750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8253   -0.9950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   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
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  1  0  0  0  0
  4 17  1  0  0  0  0
 17 11  1  1  0  0  0
 17 18  1  0  0  0  0
  2 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0235144

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1NC(=N)N2CCC(O)(O)[C@@]22NC(=N)N[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N6O3/c10-6-13-5-4(3-16)12-7(11)15-2-1-8(17,18)9(5,15)14-6/h4-5,16-18H,1-3H2,(H2,11,12)(H3,10,13,14)/t4-,5-,9-/m0/s1

> <INCHI_KEY>
VRRIYZJUSNMZMP-PJPYAQQDSA-N

> <FORMULA>
C9H16N6O3

> <MOLECULAR_WEIGHT>
256.266

> <EXACT_MASS>
256.128388399

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
24.306136911053816

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,10aS,10bS)-4-(hydroxymethyl)-2,6-diimino-decahydropyrrolo[1,2-c]purine-10,10-diol

> <JCHEM_LOGP>
-2.3474628359999996

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
12.666662246949322

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.77804176323107

> <JCHEM_PKA_STRONGEST_BASIC>
9.316438380325668

> <JCHEM_POLAR_SURFACE_AREA>
147.72

> <JCHEM_REFRACTIVITY>
80.5942

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(4R,10aS,10bS)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1H-pyrrolo[1,2-c]purine-10,10-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  N   UNK     0      -0.320  -1.303   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   1.777   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.258   2.547   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       6.258  -0.533   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       7.591  -2.843   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       4.924  -2.843   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       4.604  -4.349   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.072  -4.510   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.446  -3.103   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.112  -3.873   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.541  -1.857   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   18                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14    4   11   18                                             
CONECT   18   17    2                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Value	Source
4-(Hydroxymethyl)-2,6-diimino-decahydropyrrolo[1,2-c]purine-10,10-diol	ChEBI
DCSTX-Saxitoxin	ChEBI
Decarbamylsaxitoxin	ChEBI

Chemical Formula

C₉H₁₆N₆O₃

Average Mass

256.2660 Da

Monoisotopic Mass

256.12839 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

OC[C@@H]1NC(=N)N2CCC(O)(O)[C@@]22NC(=N)N[C@@H]12

InChI Identifier

InChI=1S/C9H16N6O3/c10-6-13-5-4(3-16)12-7(11)15-2-1-8(17,18)9(5,15)14-6/h4-5,16-18H,1-3H2,(H2,11,12)(H3,10,13,14)/t4-,5-,9-/m0/s1

InChI Key

VRRIYZJUSNMZMP-PJPYAQQDSA-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

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as saxitoxins, gonyautoxins, and derivatives. Saxitoxins, gonyautoxins, and derivatives are compounds with a structure based on a 2,6-diamino-4-methyl-pyrrolo[1,2-c]purin-10-ol skeleton.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Saxitoxins, gonyautoxins, and derivatives

Sub Class

Not Available

Direct Parent

Saxitoxins, gonyautoxins, and derivatives

Alternative Parents

Substituents

Saxitoxin-gonyautoxin skeleton
Imidazopyrimidine
Alkaloid or derivatives
1,3-diazinane
Imidazolidine
Pyrrolidine
Guanidine
Carboximidamide
Carbonyl hydrate
Organoheterocyclic compound
Azacycle
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Imine
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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

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

19975972

KEGG Compound ID

C20021

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Decarbamoylsaxitoxin

METLIN ID

Not Available

PubChem Compound

21117969

PDB ID

Not Available

ChEBI ID

133919

Good Scents ID

Not Available

References

General References

Bernard C, Harvey M, Briand JF, Bire R, Krys S, Fontaine JJ: Toxicological comparison of diverse Cylindrospermopsis raciborskii strains: evidence of liver damage caused by a French C raciborskii strain. Environ Toxicol. 2003 Jun;18(3):176-86. doi: 10.1002/tox.10112. [PubMed:12740803 ]
Negri A, Stirling D, Quilliam M, Blackburn S, Bolch C, Burton I, Eaglesham G, Thomas K, Walter J, Willis R: Three novel hydroxybenzoate saxitoxin analogues isolated from the dinoflagellate Gymnodinium catenatum. Chem Res Toxicol. 2003 Aug;16(8):1029-33. doi: 10.1021/tx034037j. [PubMed:12924931 ]
Garcia C, del Carmen Bravo M, Lagos M, Lagos N: Paralytic shellfish poisoning: post-mortem analysis of tissue and body fluid samples from human victims in the Patagonia fjords. Toxicon. 2004 Feb;43(2):149-58. doi: 10.1016/j.toxicon.2003.11.018. [PubMed:15019474 ]
Fang X, Fan X, Tang Y, Chen J, Lu J: Liquid chromatography/quadrupole time-of-flight mass spectrometry for determination of saxitoxin and decarbamoylsaxitoxin in shellfish. J Chromatogr A. 2004 May 21;1036(2):233-7. doi: 10.1016/j.chroma.2004.02.075. [PubMed:15146927 ]
Vale P, Taleb H: Assessment of the quantitative determination of paralytic shellfish poisoning toxins by pre-column derivatization and elimination of interfering compounds by solid-phase extraction. Food Addit Contam. 2005 Sep;22(9):838-46. doi: 10.1080/02652030500195247. [PubMed:16192070 ]
LOTUS database [Link]

Showing NP-Card for (3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol (NP0235144)

MOL for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

3D MOL for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

3D SDF for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

3D-SDF for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

PDB for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

3D PDB for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

SMILES for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

INCHI for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

Structure for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)

3D Structure for NP0235144 ((3as,4r,10as)-4-(hydroxymethyl)-2,6-diimino-hexahydro-1h-pyrrolo[1,2-c]purine-10,10-diol)