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Showing NP-Card for Decarbamoylsaxitoxin (NP0336844)

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Record Information
Version2.0
Created at2024-09-11 08:05:36 UTC
Updated at2024-09-11 08:05:37 UTC
NP-MRD IDNP0336844
Secondary Accession NumbersNone
Natural Product Identification
Common NameDecarbamoylsaxitoxin
Description Decarbamoylsaxitoxin was first documented in 2021 (PMID: 34564635). Based on a literature review a small amount of articles have been published on Decarbamoylsaxitoxin (PMID: 39121960) (PMID: 38786590) (PMID: 38356596).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0336844 (Decarbamoylsaxitoxin)


  Mrv2104 05262310372D          

 18 20  0  0  0  0            999 V2000
    1.6458   -2.4162    0.0000 C   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
    2.6378    0.9521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   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
    3.3523   -1.1104    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
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 N   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
    3.3523   -0.2854    0.0000 N   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
    1.1387   -1.3654    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
    1.9233    1.3646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.9092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0155   -2.4723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  8  1  1  0  0  0  0
  9  5  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  2  0  0  0  0
 11  7  2  0  0  0  0
 12  4  1  0  0  0  0
 12  7  1  0  0  0  0
 13  5  1  0  0  0  0
 13  6  1  0  0  0  0
 14  6  1  0  0  0  0
 14  9  1  0  0  0  0
 15  2  1  0  0  0  0
 15  7  1  0  0  0  0
 15  9  1  0  0  0  0
 16  3  1  0  0  0  0
 17  8  1  0  0  0  0
 18  8  1  0  0  0  0
M  END
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3D MOL for NP0336844 (Decarbamoylsaxitoxin)

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3D SDF for NP0336844 (Decarbamoylsaxitoxin)

  Mrv2104 05262310372D          

 18 20  0  0  0  0            999 V2000
    1.6458   -2.4162    0.0000 C   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
    2.6378    0.9521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   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
    3.3523   -1.1104    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
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 N   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
    3.3523   -0.2854    0.0000 N   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
    1.1387   -1.3654    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
    1.9233    1.3646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.9092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0155   -2.4723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  8  1  1  0  0  0  0
  9  5  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  2  0  0  0  0
 11  7  2  0  0  0  0
 12  4  1  0  0  0  0
 12  7  1  0  0  0  0
 13  5  1  0  0  0  0
 13  6  1  0  0  0  0
 14  6  1  0  0  0  0
 14  9  1  0  0  0  0
 15  2  1  0  0  0  0
 15  7  1  0  0  0  0
 15  9  1  0  0  0  0
 16  3  1  0  0  0  0
 17  8  1  0  0  0  0
 18  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0336844

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1NC(=N)N2CCC(O)(O)C22NC(=N)NC12

> <INCHI_IDENTIFIER>
InChI=1/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)

> <INCHI_KEY>
VRRIYZJUSNMZMP-UHFFFAOYNA-N

> <FORMULA>
C9H16N6O3

> <MOLECULAR_WEIGHT>
256.266

> <EXACT_MASS>
256.128388399

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
24.220298444270217

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
12.66666224694932

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

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0336844 (Decarbamoylsaxitoxin)
Download
PDB for NP0336844 (Decarbamoylsaxitoxin)
HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  C   UNK     0       3.072  -4.510   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.604  -4.349   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   1.777   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.446  -3.103   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.320  -1.303   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       7.591  -2.843   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       6.258  -0.533   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       4.924  -2.843   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       3.590   2.547   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.976  -3.564   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.896  -4.615   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1   15                                                       
CONECT    3    4   16                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    9   13                                                  
CONECT    6   10   13   14                                                  
CONECT    7   11   12   15                                                  
CONECT    8    1    9   17   18                                             
CONECT    9    5    8   14   15                                             
CONECT   10    6                                                            
CONECT   11    7                                                            
CONECT   12    4    7                                                       
CONECT   13    5    6                                                       
CONECT   14    6    9                                                       
CONECT   15    2    7    9                                                  
CONECT   16    3                                                            
CONECT   17    8                                                            
CONECT   18    8                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

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3D PDB for NP0336844 (Decarbamoylsaxitoxin)
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SMILES for NP0336844 (Decarbamoylsaxitoxin)
OCC1NC(=N)N2CCC(O)(O)C22NC(=N)NC12
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INCHI for NP0336844 (Decarbamoylsaxitoxin)
InChI=1/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)
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View in JSmol
SynonymsNot Available
Chemical FormulaC9H16N6O3
Average Mass256.2660 Da
Monoisotopic Mass256.12839 Da
IUPAC Name4-(hydroxymethyl)-2,6-diimino-decahydropyrrolo[1,2-c]purine-10,10-diol
Traditional Name4-(hydroxymethyl)-2,6-diimino-hexahydro-1H-pyrrolo[1,2-c]purine-10,10-diol
CAS Registry NumberNot Available
SMILES
OCC1NC(=N)N2CCC(O)(O)C22NC(=N)NC12
InChI Identifier
InChI=1/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)
InChI KeyVRRIYZJUSNMZMP-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
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-2.3ChemAxon
pKa (Strongest Acidic)10.78ChemAxon
pKa (Strongest Basic)9.32ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area147.72 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity80.59 m³·mol⁻¹ChemAxon
Polarizability24.22 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
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 LinkDecarbamoylsaxitoxin  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Alkassar M, Tudo A, Rambla-Alegre M, Ferreres L, Diogene J, Sureda FX, Campas M: First record of paralytic shellfish toxins in marine pufferfish from the Spanish Mediterranean coast using cell-based assay, automated patch clamp and HPLC-FLD. Chemosphere. 2024 Sep;364:143053. doi: 10.1016/j.chemosphere.2024.143053. Epub  2024 Aug 8. [PubMed:39121960  ] 
  2. Dirks C, Cappelli P, Blomqvist M, Ekroth S, Johansson M, Persson M, Drakare S, Pekar H, Zuberovic Muratovic A: Cyanotoxin Occurrence and Diversity in 98 Cyanobacterial Blooms from Swedish Lakes and the Baltic Sea. Mar Drugs. 2024 Apr 27;22(5):199. doi: 10.3390/md22050199. [PubMed:38786590  ] 
  3. Raposo-Garcia S, Botana AM, Rey V, Costas C, Rodriguez-Santos L, Louzao MC, Vale C, Botana LM: Analytical and functional profiles of paralytic shellfish toxins extracted from Semele proficua and Senilia senilis from Angola. Heliyon. 2024 Feb 1;10(3):e25338. doi: 10.1016/j.heliyon.2024.e25338. eCollection  2024 Feb 15. [PubMed:38356596  ] 
  4. Naknaen A, Ratsameepakai W, Suttinun O, Sukpondma Y, Khan E, Pomwised R: Microcystis Sp. Co-Producing Microcystin and Saxitoxin from Songkhla Lake Basin, Thailand. Toxins (Basel). 2021 Sep 8;13(9):631. doi: 10.3390/toxins13090631. [PubMed:34564635  ]