NP-MRD: Showing NP-Card for (2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol (NP0263843)

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Record Information

Version

2.0

Created at

2022-09-08 07:09:09 UTC

Updated at

2022-09-08 07:09:09 UTC

NP-MRD ID

NP0263843

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol

Description

Adenosine, 2-chloro-5'-deoxy-2'-C-methyl- belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. (2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol is found in Trachycladus laevispirulifer. Based on a literature review very few articles have been published on Adenosine, 2-chloro-5'-deoxy-2'-C-methyl-.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 36  0  0  0  0  0  0  0  0999 V2000
   -3.4075   -1.5844    0.1939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4664   -0.6266    0.8550 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1223   -0.9346    0.6057 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5158    0.2508    0.9014 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8984    0.2965    0.6682 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6374    1.3506    1.0628 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8996    1.1507    0.7340 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9989   -0.0300    0.1242 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0669   -0.7475   -0.4289 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3437   -0.1605   -0.3659 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7797   -1.9284   -0.9689 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5295   -2.4263   -0.9920 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3297   -4.0057   -1.7475 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.4802   -1.7529   -0.4644 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7279   -0.5600    0.0887 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2787    1.2082   -0.0218 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0349    0.8780   -1.4660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0618    2.5185    0.3070 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7067    0.7493    0.2972 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2592    1.6151    1.2459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0927   -2.6341    0.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3780   -1.5259    0.7649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6910   -1.2618   -0.8475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6929   -0.6031    1.9456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7476    0.5716    1.9329 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2963    2.2581    1.5794 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8384    0.0017    0.5371 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8188    0.1243   -1.2362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4286   -0.1633   -1.6249 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0237    0.9417   -1.7659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6558    1.5388   -2.0765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6019    2.9480   -0.4792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3214    0.7527   -0.6171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2059    1.7903    1.0299 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
  4 16  1  0
 16 17  1  0
 16 18  1  6
 16 19  1  0
 19 20  1  0
 19  2  1  0
 15  5  1  0
 15  8  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  1
  4 25  1  1
  6 26  1  0
 10 27  1  0
 10 28  1  0
 17 29  1  0
 17 30  1  0
 17 31  1  0
 18 32  1  0
 19 33  1  6
 20 34  1  0
M  END


  Mrv1652309082209092D          

 20 22  0  0  1  0            999 V2000
   -0.5683   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.9521    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 N   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
    4.0668   -1.5229    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 N   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
    1.3687   -2.8174    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9818   -2.2654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9818   -3.3695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1387   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  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
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
  8 15  1  0  0  0  0
  5 15  1  0  0  0  0
  4 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  6  0  0  0
 16 19  1  0  0  0  0
  2 19  1  0  0  0  0
 19 20  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0263843

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H14ClN5O3/c1-4-6(18)11(2,19)9(20-4)17-3-14-5-7(13)15-10(12)16-8(5)17/h3-4,6,9,18-19H,1-2H3,(H2,13,15,16)/t4-,6-,9-,11-/m1/s1

> <INCHI_KEY>
VGXNTNGMCOCQAZ-GITKWUPZSA-N

> <FORMULA>
C11H14ClN5O3

> <MOLECULAR_WEIGHT>
299.72

> <EXACT_MASS>
299.078517

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
28.25353520928369

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R,4R,5R)-2-(6-amino-2-chloro-9H-purin-9-yl)-3,5-dimethyloxolane-3,4-diol

> <JCHEM_LOGP>
0.14507310866666678

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.856294783273775

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.372228405502884

> <JCHEM_PKA_STRONGEST_BASIC>
1.3040737045377984

> <JCHEM_POLAR_SURFACE_AREA>
119.31000000000002

> <JCHEM_REFRACTIVITY>
71.78869999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5R)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.061  -6.934   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.185  -6.029   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.185  -4.489   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       4.924   1.777   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       6.258  -0.533   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   13 Cl   UNK     0       7.591  -2.843   0.000  0.00  0.00          Cl+0
HETATM   14  N   UNK     0       4.924  -2.843   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.555  -5.259   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.699  -4.229   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.699  -6.290   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.650  -6.505   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.126  -7.970   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   16                                                  
CONECT    5    4    6   15                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   15                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    8    5                                                  
CONECT   16    4   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16    2   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₄ClN₅O₃

Average Mass

299.7200 Da

Monoisotopic Mass

299.07852 Da

IUPAC Name

(2R,3R,4R,5R)-2-(6-amino-2-chloro-9H-purin-9-yl)-3,5-dimethyloxolane-3,4-diol

Traditional Name

(2R,3R,4R,5R)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C11H14ClN5O3/c1-4-6(18)11(2,19)9(20-4)17-3-14-5-7(13)15-10(12)16-8(5)17/h3-4,6,9,18-19H,1-2H3,(H2,13,15,16)/t4-,6-,9-,11-/m1/s1

InChI Key

VGXNTNGMCOCQAZ-GITKWUPZSA-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
Trachycladus laevispirulifer	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
6-aminopurine
Imidazopyrimidine
Purine
Aminopyrimidine
2-halopyrimidine
Halopyrimidine
Aryl chloride
Aryl halide
Imidolactam
N-substituted imidazole
Pyrimidine
Heteroaromatic compound
Azole
Imidazole
Tertiary alcohol
Oxolane
Secondary alcohol
1,2-diol
Organoheterocyclic compound
Azacycle
Oxacycle
Organohalogen compound
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organochloride
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
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	0.15	ChemAxon
pKa (Strongest Acidic)	12.37	ChemAxon
pKa (Strongest Basic)	1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	119.31 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	71.79 m³·mol⁻¹	ChemAxon
Polarizability	28.25 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

8442256

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10266777

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,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol (NP0263843)

MOL for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

3D MOL for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

3D SDF for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

3D-SDF for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

PDB for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

3D PDB for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

SMILES for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

INCHI for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

Structure for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)

3D Structure for NP0263843 ((2r,3r,4r,5r)-2-(6-amino-2-chloropurin-9-yl)-3,5-dimethyloxolane-3,4-diol)