NP-MRD: Showing NP-Card for [(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol (NP0240837)

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Record Information

Version

2.0

Created at

2022-09-07 00:45:08 UTC

Updated at

2022-09-07 00:45:08 UTC

NP-MRD ID

NP0240837

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol

Description

Synadenol belongs to the class of organic compounds known as 6-aminopurines. These are purines that carry an amino group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring. [(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol is found in Euphorbia bicompacta. [(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol was first documented in 2002 (PMID: 12406510). Based on a literature review very few articles have been published on Synadenol (PMID: 14561099).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072202452D          

 16 18  0  0  0  0            999 V2000
    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
    2.8616   -1.9076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2485   -2.4596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9935   -3.2442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5455   -3.8573    0.0000 O   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  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
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0240837

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C2N=CN(\C=C3/CC3CO)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H11N5O/c11-9-8-10(13-4-12-9)15(5-14-8)2-6-1-7(6)3-16/h2,4-5,7,16H,1,3H2,(H2,11,12,13)/b6-2+

> <INCHI_KEY>
BOCARSGZHMZWCE-QHHAFSJGSA-N

> <FORMULA>
C10H11N5O

> <MOLECULAR_WEIGHT>
217.232

> <EXACT_MASS>
217.096359994

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
22.200156775699604

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2E)-2-[(6-amino-9H-purin-9-yl)methylidene]cyclopropyl]methanol

> <JCHEM_LOGP>
-0.7080976909999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.53367740707946

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.41104886821012

> <JCHEM_PKA_STRONGEST_BASIC>
3.9648555237570604

> <JCHEM_POLAR_SURFACE_AREA>
89.85000000000001

> <JCHEM_REFRACTIVITY>
59.7418

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(2E)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  N   UNK     0       6.121   3.850   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       7.454   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       6.121  -0.770   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.877  -3.085   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.342  -3.561   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.197  -4.591   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.721  -6.056   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.752  -7.200   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12   14                                                       
CONECT   14   13   12   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₁N₅O

Average Mass

217.2320 Da

Monoisotopic Mass

217.09636 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

NC1=C2N=CN(\C=C3/CC3CO)C2=NC=N1

InChI Identifier

InChI=1S/C10H11N5O/c11-9-8-10(13-4-12-9)15(5-14-8)2-6-1-7(6)3-16/h2,4-5,7,16H,1,3H2,(H2,11,12,13)/b6-2+

InChI Key

BOCARSGZHMZWCE-QHHAFSJGSA-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
Euphorbia bicompacta	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 6-aminopurines. These are purines that carry an amino group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

6-aminopurines

Alternative Parents

Substituents

6-aminopurine
Aminopyrimidine
N-substituted imidazole
Pyrimidine
Imidolactam
Azole
Imidazole
Heteroaromatic compound
Azacycle
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Alcohol
Organic nitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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

5017102

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6531437

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Wang R, Harada S, Mitsuya H, Zemlicka J: Inhibition of human immunodeficiency virus reverse transcriptase by synadenol triphosphate and its E-isomer. J Med Chem. 2003 Oct 23;46(22):4799-802. doi: 10.1021/jm030048y. [PubMed:14561099 ]
Baldanti F, Sarasini A, Drach JC, Zemlicka J, Gerna G: Z-isomers of 2-hydroxymethylcyclopropylidenemethyl adenine (synadenol) and guanine (synguanol) are active against ganciclovir- and foscarnet-resistant human cytomegalovirus UL97 mutants. Antiviral Res. 2002 Dec;56(3):273-8. doi: 10.1016/s0166-3542(02)00129-8. [PubMed:12406510 ]
LOTUS database [Link]

Showing NP-Card for [(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol (NP0240837)

MOL for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

3D MOL for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

3D SDF for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

3D-SDF for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

PDB for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

3D PDB for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

SMILES for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

INCHI for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

Structure for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)

3D Structure for NP0240837 ([(2e)-2-[(6-aminopurin-9-yl)methylidene]cyclopropyl]methanol)