NP-MRD: Showing NP-Card for Charine (NP0049523)

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Record Information

Version

2.0

Created at

2022-03-17 21:13:53 UTC

Updated at

2022-03-17 21:13:53 UTC

NP-MRD ID

NP0049523

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Charine

Description

Charine belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Charine is a strong basic compound (based on its pKa). Outside of the human body, Charine has been detected, but not quantified in, bitter gourds and fruits. This could make charine a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061311272D          

 19 20  0  0  0  0            999 V2000
   -2.4358    2.4585    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1508    2.0460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8658    2.4585    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5795    2.0460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2945    2.4585    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8658   -0.0151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8658    0.8085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1508    1.2210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4358    0.8085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4358   -0.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7222   -0.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5795    1.2210    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1508   -0.4290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1508   -1.2526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4358   -2.4901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4358   -1.6665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7222   -1.2526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0071   -1.6665    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0071   -0.0151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  8  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4 12  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7 12  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 13  1  0  0  0  0
 11 17  1  0  0  0  0
 11 19  1  0  0  0  0
 13 14  1  0  0  0  0
 14 16  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049523

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC(O)=C(OC2OCC(O)C(O)C2O)C(N)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N4O6/c10-6-5(7(17)13-9(11)12-6)19-8-4(16)3(15)2(14)1-18-8/h2-4,8,14-16H,1H2,(H5,10,11,12,13,17)

> <INCHI_KEY>
VSPBJCAGAJBGKS-UHFFFAOYSA-N

> <FORMULA>
C9H14N4O6

> <MOLECULAR_WEIGHT>
274.2307

> <EXACT_MASS>
274.0913342

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
24.604052824589935

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2,4-diamino-6-hydroxypyrimidin-5-yl)oxy]oxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.96

> <JCHEM_LOGP>
-1.9852791646666665

> <ALOGPS_LOGS>
-1.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.959672539535301

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.17473567630894

> <JCHEM_PKA_STRONGEST_BASIC>
3.1643745160179932

> <JCHEM_POLAR_SURFACE_AREA>
177.2

> <JCHEM_REFRACTIVITY>
62.8398

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.54e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2,4-diamino-6-hydroxypyrimidin-5-yl)oxy]oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  N   UNK     0      -4.547   4.589   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -5.881   3.819   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -7.216   4.589   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -8.548   3.819   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -9.883   4.589   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      -7.216  -0.028   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -7.216   1.509   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.881   2.279   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.547   1.509   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.547  -0.028   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.215  -0.801   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -8.548   2.279   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      -5.881  -0.801   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -5.881  -2.338   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.547  -4.648   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -4.547  -3.111   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.215  -2.338   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.880  -3.111   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.880  -0.028   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4                                                            
CONECT    6    7                                                            
CONECT    7    6    8   12                                                  
CONECT    8    2    7    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   17   19                                                  
CONECT   12    4    7                                                       
CONECT   13   10   14                                                       
CONECT   14   13   16                                                       
CONECT   15   16                                                            
CONECT   16   14   15   17                                                  
CONECT   17   11   16   18                                                  
CONECT   18   17                                                            
CONECT   19   11                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₄N₄O₆

Average Mass

274.2307 Da

Monoisotopic Mass

274.09133 Da

IUPAC Name

2-[(2,4-diamino-6-hydroxypyrimidin-5-yl)oxy]oxane-3,4,5-triol

Traditional Name

2-[(2,4-diamino-6-hydroxypyrimidin-5-yl)oxy]oxane-3,4,5-triol

CAS Registry Number

165171-52-8

SMILES

NC1=NC(O)=C(OC2OCC(O)C(O)C2O)C(N)=N1

InChI Identifier

InChI=1S/C9H14N4O6/c10-6-5(7(17)13-9(11)12-6)19-8-4(16)3(15)2(14)1-18-8/h2-4,8,14-16H,1H2,(H5,10,11,12,13,17)

InChI Key

VSPBJCAGAJBGKS-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Momordica charantia	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

O-glycosyl compound
Pentose monosaccharide
Aminopyrimidine
Hydroxypyrimidine
Monosaccharide
Oxane
Pyrimidine
Imidolactam
Heteroaromatic compound
Secondary alcohol
Acetal
Oxacycle
Azacycle
Polyol
Organoheterocyclic compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Alcohol
Amine
Organic nitrogen compound
Primary amine
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
logP	-2	ALOGPS
logP	-2	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	12.17	ChemAxon
pKa (Strongest Basic)	3.16	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	177.2 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	62.84 m³·mol⁻¹	ChemAxon
Polarizability	24.6 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0039877

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB019536

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

131752741

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Charine (NP0049523)

MOL for NP0049523 (Charine)

3D MOL for NP0049523 (Charine)

3D SDF for NP0049523 (Charine)

3D-SDF for NP0049523 (Charine)

PDB for NP0049523 (Charine)

3D PDB for NP0049523 (Charine)

SMILES for NP0049523 (Charine)

INCHI for NP0049523 (Charine)

Structure for NP0049523 (Charine)

3D Structure for NP0049523 (Charine)