NP-MRD: Showing NP-Card for (1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol (NP0260960)

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Record Information

Version

2.0

Created at

2022-09-08 03:16:53 UTC

Updated at

2022-09-08 03:16:53 UTC

NP-MRD ID

NP0260960

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol

Description

(1R,2S,3R)-1-{6-[(2R,3S)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms. (1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol is found in Gynura divaricata. Based on a literature review very few articles have been published on (1R,2S,3R)-1-{6-[(2R,3S)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 41 41  0  0  0  0  0  0  0  0999 V2000
   -3.3614    2.1350   -1.4961 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5296    1.5752   -1.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5360    0.0839   -1.0431 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.8454   -0.2787   -0.5824 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5119   -0.5818   -0.1883 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7071   -0.1165    1.1292 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1349   -0.2914   -0.6350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1053   -0.9936    0.2181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4080   -1.8193    1.2587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3921   -2.3989    1.9652 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8985   -2.1826    1.6687 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1870   -1.3497    0.6191 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5858   -1.0565    0.2244 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6275   -1.1597   -1.1605 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9109    0.2978    0.7612 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0272    1.2360    0.2523 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3411    0.6968    0.7536 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4202    1.8652    1.5686 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9023    1.1103   -0.5691 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8946    0.0372   -1.4386 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1918   -0.7805   -0.0746 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0570    2.8855   -0.9045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3582    1.9546   -1.6993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7049    1.9583    0.0121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4976   -0.2699   -2.0870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7612   -1.2350   -0.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7383   -1.6768   -0.2127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0437    0.5705    1.3718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9924   -0.5137   -1.7077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9210    0.8016   -0.4691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4302   -2.0046    1.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6889   -2.6688    2.2627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2333   -1.8569    0.6528 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8298   -0.6686   -1.4995 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6275    0.2388    1.8710 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0078    1.2486   -0.7384 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -0.0730    1.2351 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9861    2.5723    0.9956 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9717    1.4127   -0.4536 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3988    2.0074   -0.9902 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3544   -0.7110   -0.9799 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 21  2  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 21  8  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  6
  4 26  1  0
  5 27  1  1
  6 28  1  0
  7 29  1  0
  7 30  1  0
  9 31  1  0
 11 32  1  0
 13 33  1  1
 14 34  1  0
 15 35  1  1
 16 36  1  0
 17 37  1  1
 18 38  1  0
 19 39  1  0
 19 40  1  0
 20 41  1  0
M  END


  Mrv1652309082205162D          

 21 21  0  0  1  0            999 V2000
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 12 21  2  0  0  0  0
  8 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0260960

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H](O)[C@H](O)CC1=CN=CC(=N1)[C@@H](O)[C@H](O)[C@H](O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C12H20N2O7/c15-4-9(18)8(17)1-6-2-13-3-7(14-6)11(20)12(21)10(19)5-16/h2-3,8-12,15-21H,1,4-5H2/t8-,9+,10-,11-,12-/m1/s1

> <INCHI_KEY>
MBHUNOHYVYVNIP-IYKVGLELSA-N

> <FORMULA>
C12H20N2O7

> <MOLECULAR_WEIGHT>
304.299

> <EXACT_MASS>
304.127050992

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
29.86312913985256

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,3R)-1-{6-[(2R,3S)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol

> <JCHEM_LOGP>
-4.596327548

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.090272546114242

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.283459908690652

> <JCHEM_PKA_STRONGEST_BASIC>
0.3822068186018085

> <JCHEM_POLAR_SURFACE_AREA>
167.39

> <JCHEM_REFRACTIVITY>
68.9186

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3R)-1-{6-[(2R,3S)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.000   1.540   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   21                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19                                                            
CONECT   21   12    8                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₂₀N₂O₇

Average Mass

304.2990 Da

Monoisotopic Mass

304.12705 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

OC[C@H](O)[C@H](O)CC1=CN=CC(=N1)[C@@H](O)[C@H](O)[C@H](O)CO

InChI Identifier

InChI=1S/C12H20N2O7/c15-4-9(18)8(17)1-6-2-13-3-7(14-6)11(20)12(21)10(19)5-16/h2-3,8-12,15-21H,1,4-5H2/t8-,9+,10-,11-,12-/m1/s1

InChI Key

MBHUNOHYVYVNIP-IYKVGLELSA-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
Gynura divaricata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrazines

Direct Parent

Pyrazines

Alternative Parents

Substituents

Pyrazine
Sugar alcohol
Heteroaromatic compound
Secondary alcohol
Polyol
Azacycle
Aromatic alcohol
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Primary alcohol
Alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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

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

29789373

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162990888

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol (NP0260960)

MOL for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

3D MOL for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

3D SDF for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

3D-SDF for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

PDB for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

3D PDB for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

SMILES for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

INCHI for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

Structure for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)

3D Structure for NP0260960 ((1r,2s,3r)-1-{6-[(2r,3s)-2,3,4-trihydroxybutyl]pyrazin-2-yl}butane-1,2,3,4-tetrol)