NP-MRD: Showing NP-Card for Convicine (NP0047134)

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Record Information

Version

2.0

Created at

2022-03-17 20:35:12 UTC

Updated at

2022-03-17 20:35:12 UTC

NP-MRD ID

NP0047134

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Convicine

Description

Convicine is found in Vicia sativa .

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241221182D          

 21 22  0  0  1  0            999 V2000
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  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   -2.4750    0.0000 C   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
   -1.4289   -2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  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   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  2  0  0  0  0
 10 17  1  0  0  0  0
  5 18  1  1  0  0  0
  4 19  1  6  0  0  0
  3 20  1  1  0  0  0
  1 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047134

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N3O8/c11-7-6(8(18)13-10(19)12-7)21-9-5(17)4(16)3(15)2(1-14)20-9/h2-5,9,14-17H,1H2,(H4,11,12,13,18,19)/t2-,3-,4+,5-,9+/m1/s1

> <INCHI_KEY>
JJWYIMQKLTVAGZ-SYCVNHKBSA-N

> <FORMULA>
C10H15N3O8

> <MOLECULAR_WEIGHT>
305.2414

> <EXACT_MASS>
305.085914471

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
26.8157665335239

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-2.00

> <JCHEM_LOGP>
-3.9044494516666663

> <ALOGPS_LOGS>
-0.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.119948398617566

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.154510860372817

> <JCHEM_PKA_STRONGEST_BASIC>
1.6490477529197856

> <JCHEM_POLAR_SURFACE_AREA>
183.59999999999997

> <JCHEM_REFRACTIVITY>
73.28599999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.10e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-amino-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1,3-dihydropyrimidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -2.667  -4.620   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      -1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0      -1.334  -6.930   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2   21                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4   20                                                  
CONECT    4    3    5   19                                                  
CONECT    5    4    6   18                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    9   16                                                  
CONECT   16   15                                                            
CONECT   17   10                                                            
CONECT   18    5                                                            
CONECT   19    4                                                            
CONECT   20    3                                                            
CONECT   21    1                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₅N₃O₈

Average Mass

305.2414 Da

Monoisotopic Mass

305.08591 Da

IUPAC Name

6-amino-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

6-amino-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1,3-dihydropyrimidine-2,4-dione

CAS Registry Number

19286-37-4

SMILES

NC1=C(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC(=O)N1

InChI Identifier

InChI=1S/C10H15N3O8/c11-7-6(8(18)13-10(19)12-7)21-9-5(17)4(16)3(15)2(1-14)20-9/h2-5,9,14-17H,1H2,(H4,11,12,13,18,19)/t2-,3-,4+,5-,9+/m1/s1

InChI Key

JJWYIMQKLTVAGZ-SYCVNHKBSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Vicia faba	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Vicia sativa	Plant	KNApSAcK

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

Hexose monosaccharide
O-glycosyl compound
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Monosaccharide
Oxane
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Lactam
Urea
Secondary alcohol
Acetal
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Amine
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organonitrogen compound
Organic nitrogen compound
Primary alcohol
Primary amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

glycoside (CHEBI:3867 )

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	-3.9	ChemAxon
logS	-0.78	ALOGPS
pKa (Strongest Acidic)	9.15	ChemAxon
pKa (Strongest Basic)	1.65	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	183.6 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	73.29 m³·mol⁻¹	ChemAxon
Polarizability	26.82 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB007483

KNApSAcK ID

C00001494

Chemspider ID

Not Available

KEGG Compound ID

C08430

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

88000

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Convicine (NP0047134)

MOL for NP0047134 (Convicine)

3D MOL for NP0047134 (Convicine)

3D SDF for NP0047134 (Convicine)

3D-SDF for NP0047134 (Convicine)

PDB for NP0047134 (Convicine)

3D PDB for NP0047134 (Convicine)

SMILES for NP0047134 (Convicine)

INCHI for NP0047134 (Convicine)

Structure for NP0047134 (Convicine)

3D Structure for NP0047134 (Convicine)