NP-MRD: Showing NP-Card for (2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol (NP0239158)

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Record Information

Version

2.0

Created at

2022-09-06 22:41:08 UTC

Updated at

2022-09-06 22:41:08 UTC

NP-MRD ID

NP0239158

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol

Description

(2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol is found in Streptomyces angustmyceticus.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 35  0  0  0  0  0  0  0  0999 V2000
   -2.9857    2.3810    0.3166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2544    1.2651    0.1959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3655    0.9511   -0.8174 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8959   -0.3789   -0.6846 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6899   -1.0594   -2.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2333   -2.3444   -1.7580 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3538   -0.4319    0.0410 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6836   -1.1021    1.1537 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9632   -0.8687    1.4930 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4933   -0.0210    0.5794 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7582    0.5395    0.4518 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7705    0.2292    1.4149 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9774    1.3559   -0.5800 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9949    1.6209   -1.4640 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7674    1.0792   -1.3434 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4756    0.2390   -0.3160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9776   -1.0224    0.1429 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1483   -1.2283   -0.5498 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2455    0.1172    1.1374 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4704   -0.0823    1.7444 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9487    3.1727   -0.3947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6391    2.4831    1.1684 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1240   -0.5167   -2.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5699   -1.0356   -2.6606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7768   -2.8130   -1.0936 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0350   -1.7391    1.7097 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5191   -0.0899    2.3766 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7809    0.3120    1.1867 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2476    2.2997   -2.2852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6859   -1.9439    0.6336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2452   -0.6872   -1.3595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4077    0.2453    1.8415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4047   -0.9262    2.2584 H   0  0  0  0  0  0  0  0  0  0  0  0
 19 20  1  0
 19  2  1  0
  2  1  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  6
  5  6  1  0
  4  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
  4 17  1  0
 17 18  1  0
 17 19  1  0
 16  7  1  0
 16 10  1  0
 19 32  1  1
 20 33  1  0
  1 21  1  0
  1 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  8 26  1  0
 12 27  1  0
 12 28  1  0
 14 29  1  0
 17 30  1  1
 18 31  1  0
M  END


  Mrv0541 05311207052D          

 22 24  0  0  0  0            999 V2000
    0.8518   -2.0637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1301    0.4064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0233   -1.2567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7770   -0.9211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6908   -0.1006    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5373   -0.0785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4915   -1.3336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3038    0.4514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4713   -0.6436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7338   -1.7450    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4610   -0.3963    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  2  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  2  1  6  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13  3  2  0  0  0  0
 13  9  1  0  0  0  0
 14  3  1  0  0  0  0
 14 10  2  0  0  0  0
 15  4  2  0  0  0  0
 15  6  1  0  0  0  0
 16  4  1  0  0  0  0
 16 10  1  0  0  0  0
 11 16  1  1  0  0  0
 17  2  1  0  0  0  0
  7 18  1  6  0  0  0
  8 19  1  6  0  0  0
 20  5  1  0  0  0  0
 20 11  1  0  0  0  0
  7 21  1  1  0  0  0
  8 22  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0239158

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(O)C(=C)O[C@@](CO)(N2C=NC3=C(N)N=CN=C23)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C11H13N5O4/c1-5-7(18)8(19)11(2-17,20-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-4,7-8,17-19H,1-2H2,(H2,12,13,14)/t7-,8-,11-/m1/s1

> <INCHI_KEY>
UZSSGAOAYPICBZ-SOCHQFKDSA-N

> <FORMULA>
C11H13N5O4

> <MOLECULAR_WEIGHT>
279.252

> <EXACT_MASS>
279.096753929

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
26.120116365250112

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S)-2-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol

> <ALOGPS_LOGP>
-0.72

> <JCHEM_LOGP>
-1.6962181496666666

> <ALOGPS_LOGS>
-1.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.482105464573625

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.180498359632436

> <JCHEM_PKA_STRONGEST_BASIC>
4.963356167385309

> <JCHEM_POLAR_SURFACE_AREA>
139.54

> <JCHEM_REFRACTIVITY>
68.3957

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.01e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 31-MAY-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-MAY-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2   11   17                                                       
CONECT    3   13   14                                                       
CONECT    4   15   16                                                       
CONECT    5    1    7   20                                                  
CONECT    6    9   10   15                                                  
CONECT    7    5    8   18   21                                             
CONECT    8    7   11   19   22                                             
CONECT    9    6   12   13                                                  
CONECT   10    6   14   16                                                  
CONECT   11    2    8   16   20                                             
CONECT   12    9                                                            
CONECT   13    3    9                                                       
CONECT   14    3   10                                                       
CONECT   15    4    6                                                       
CONECT   16    4   10   11                                                  
CONECT   17    2                                                            
CONECT   18    7                                                            
CONECT   19    8                                                            
CONECT   20    5   11                                                       
CONECT   21    7                                                            
CONECT   22    8                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
Decoyinin	MeSH
Angustmycin a	MeSH
Decoyinine	MeSH

Chemical Formula

C₁₁H₁₃N₅O₄

Average Mass

279.2520 Da

Monoisotopic Mass

279.09675 Da

IUPAC Name

(2R,3R,4S)-2-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol

Traditional Name

(2R,3R,4S)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)C(=C)O[C@@](CO)(N2C=NC3=C(N)N=CN=C23)[C@]1([H])O

InChI Identifier

InChI=1S/C11H13N5O4/c1-5-7(18)8(19)11(2-17,20-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-4,7-8,17-19H,1-2H2,(H2,12,13,14)/t7-,8-,11-/m1/s1

InChI Key

UZSSGAOAYPICBZ-SOCHQFKDSA-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
Streptomyces angustmyceticus	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
Monosaccharide
N-substituted imidazole
Imidolactam
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organooxygen compound
Organonitrogen compound
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Amine
Primary alcohol
Primary 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
logP	-0.72	ALOGPS
logP	-1.7	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	12.18	ChemAxon
pKa (Strongest Basic)	4.96	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	139.54 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	68.4 m³·mol⁻¹	ChemAxon
Polarizability	26.12 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

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

121578

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol (NP0239158)

MOL for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

3D MOL for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

3D SDF for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

3D-SDF for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

PDB for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

3D PDB for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

SMILES for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

INCHI for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

Structure for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)

3D Structure for NP0239158 ((2r,3r,4s)-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylideneoxolane-3,4-diol)