NP-MRD: Showing NP-Card for 2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0221851)

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Record Information

Version

2.0

Created at

2022-09-05 23:32:01 UTC

Updated at

2022-09-05 23:32:01 UTC

NP-MRD ID

NP0221851

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

2-{6-[(4-Hydroxy-3-methylbut-2-en-1-yl)amino]-9H-purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). 2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Arabidopsis thaliana. 2-{6-[(4-Hydroxy-3-methylbut-2-en-1-yl)amino]-9H-purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol is a strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004241523212D          

 27 29  0  0  0  0            999 V2000
    5.4223    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0769   -1.6527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8220   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0150   -2.6088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4630   -1.9957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7179   -1.2111    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3440   -2.1672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5989   -2.9519    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7601   -3.3934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3740   -3.0504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8839   -1.4811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    4.9500    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
  3  4  1  4  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  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
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
 14 15  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
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 23  1  0  0  0  0
 17 24  1  0  0  0  0
 16 25  1  0  0  0  0
  2 26  1  0  0  0  0
 26 27  1  0  0  0  0
M  END


  Mrv1533004241523212D          

 27 29  0  0  0  0            999 V2000
    5.4223    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0769   -1.6527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8220   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0150   -2.6088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4630   -1.9957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7179   -1.2111    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3440   -2.1672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5989   -2.9519    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7601   -3.3934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3740   -3.0504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8839   -1.4811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    4.9500    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
  3  4  1  4  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  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
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
 14 15  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
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 23  1  0  0  0  0
 17 24  1  0  0  0  0
 16 25  1  0  0  0  0
  2 26  1  0  0  0  0
 26 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0221851

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CO)=CCNC1=NC=NC2=C1N=CN2C1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C16H23N5O6/c1-8(4-22)2-3-17-14-10-15(19-6-18-14)21(7-20-10)16-13(26)12(25)11(24)9(5-23)27-16/h2,6-7,9,11-13,16,22-26H,3-5H2,1H3,(H,17,18,19)

> <INCHI_KEY>
VYRAJOITMBSQSE-UHFFFAOYSA-N

> <FORMULA>
C16H23N5O6

> <MOLECULAR_WEIGHT>
381.389

> <EXACT_MASS>
381.164833481

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
39.039589081624605

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]-9H-purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.71

> <JCHEM_LOGP>
-2.3391197993333335

> <ALOGPS_LOGS>
-1.77

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.267143682650989

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.357289457507026

> <JCHEM_PKA_STRONGEST_BASIC>
4.845112298327643

> <JCHEM_POLAR_SURFACE_AREA>
166.01

> <JCHEM_REFRACTIVITY>
95.54439999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0      10.122   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.788   6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.454   6.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.454   4.620   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       6.121   3.850   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       7.454   1.540   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       6.121  -0.770   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.877  -3.085   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.401  -4.550   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.895  -4.870   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.864  -3.725   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.340  -2.261   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -0.642  -4.046   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.118  -5.510   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.419  -6.334   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.432  -5.694   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.383  -2.765   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       8.788   8.470   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       7.454   9.240   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10    6   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   10   15                                                  
CONECT   15   14   16   20                                                  
CONECT   16   15   17   25                                                  
CONECT   17   16   18   24                                                  
CONECT   18   17   19   23                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19   15                                                       
CONECT   21   19   22                                                       
CONECT   22   21                                                            
CONECT   23   18                                                            
CONECT   24   17                                                            
CONECT   25   16                                                            
CONECT   26    2   27                                                       
CONECT   27   26                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₂₃N₅O₆

Average Mass

381.3890 Da

Monoisotopic Mass

381.16483 Da

IUPAC Name

2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]-9H-purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CC(CO)=CCNC1=NC=NC2=C1N=CN2C1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C16H23N5O6/c1-8(4-22)2-3-17-14-10-15(19-6-18-14)21(7-20-10)16-13(26)12(25)11(24)9(5-23)27-16/h2,6-7,9,11-13,16,22-26H,3-5H2,1H3,(H,17,18,19)

InChI Key

VYRAJOITMBSQSE-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Arabidopsis thaliana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

Hexose monosaccharide
N-glycosyl compound
6-alkylaminopurine
6-aminopurine
Purine
Imidazopyrimidine
Aminopyrimidine
Imidolactam
Pyrimidine
Monosaccharide
Oxane
N-substituted imidazole
Heteroaromatic compound
Azole
Imidazole
Secondary alcohol
Polyol
Organoheterocyclic compound
Azacycle
Oxacycle
Primary alcohol
Hydrocarbon derivative
Organic nitrogen compound
Alcohol
Amine
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

a glucoside (CPD-4619 )

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	-0.71	ALOGPS
logP	-2.3	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	12.36	ChemAxon
pKa (Strongest Basic)	4.85	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	166.01 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	95.54 m³·mol⁻¹	ChemAxon
Polarizability	39.04 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

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

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

53399083

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0221851)

MOL for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0221851 (2-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}-6-(hydroxymethyl)oxane-3,4,5-triol)