NP-MRD: Showing NP-Card for (2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0171902)

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Record Information

Version

2.0

Created at

2022-09-03 08:36:42 UTC

Updated at

2022-09-03 08:36:42 UTC

NP-MRD ID

NP0171902

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

62512-97-4 Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. (2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Arabidopsis thaliana. Based on a literature review very few articles have been published on 62512-97-4.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032210362D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309032210362D          

 36 39  0  0  1  0            999 V2000
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 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 26 35  1  0  0  0  0
 35 36  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0171902

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)=C/CNC1=C2N=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C21H31N5O10/c1-9(6-34-21-17(33)15(31)13(29)11(5-28)36-21)2-3-22-18-12-19(24-7-23-18)26(8-25-12)20-16(32)14(30)10(4-27)35-20/h2,7-8,10-11,13-17,20-21,27-33H,3-6H2,1H3,(H,22,23,24)/b9-2+/t10-,11-,13-,14-,15+,16-,17-,20-,21-/m1/s1

> <INCHI_KEY>
MVMBTNNVZQRZQT-BPDSZQNASA-N

> <FORMULA>
C21H31N5O10

> <MOLECULAR_WEIGHT>
513.504

> <EXACT_MASS>
513.207092218

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
51.944102783406244

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(2E)-4-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.33

> <JCHEM_LOGP>
-3.4796205029999996

> <ALOGPS_LOGS>
-1.91

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.576777811874674

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.016728503284472

> <JCHEM_PKA_STRONGEST_BASIC>
3.701553967048062

> <JCHEM_POLAR_SURFACE_AREA>
224.92999999999995

> <JCHEM_REFRACTIVITY>
121.9952

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.29e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(2E)-4-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         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  O   UNK     0       3.752  -3.186   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.846  -4.432   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.322  -5.897   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.292  -7.041   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       1.382  -3.956   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.136  -4.862   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.382  -2.416   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       0.136  -1.511   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       8.788   8.470   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       7.454   9.240   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       7.454  10.780   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       6.121  11.550   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       6.121  13.090   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.787  13.860   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.787  15.400   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       7.454  13.860   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       7.454  15.400   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       8.788  13.090   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      10.122  13.860   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       8.788  11.550   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      10.122  10.780   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   24                                                  
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   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   15   23                                                  
CONECT   23   22                                                            
CONECT   24    2   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   35                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   26   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₁N₅O₁₀

Average Mass

513.5040 Da

Monoisotopic Mass

513.20709 Da

IUPAC Name

(2R,3R,4S,5S,6R)-2-{[(2E)-4-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2R,3R,4S,5S,6R)-2-{[(2E)-4-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

C\C(CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)=C/CNC1=C2N=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C2=NC=N1

InChI Identifier

InChI=1S/C21H31N5O10/c1-9(6-34-21-17(33)15(31)13(29)11(5-28)36-21)2-3-22-18-12-19(24-7-23-18)26(8-25-12)20-16(32)14(30)10(4-27)35-20/h2,7-8,10-11,13-17,20-21,27-33H,3-6H2,1H3,(H,22,23,24)/b9-2+/t10-,11-,13-,14-,15+,16-,17-,20-,21-/m1/s1

InChI Key

MVMBTNNVZQRZQT-BPDSZQNASA-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
Arabidopsis thaliana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Glycosyl compound
N-glycosyl compound
O-glycosyl compound
6-alkylaminopurine
6-aminopurine
Imidazopyrimidine
Purine
Aminopyrimidine
Secondary aliphatic/aromatic amine
Fatty acyl
Monosaccharide
N-substituted imidazole
Oxane
Imidolactam
Pyrimidine
Tetrahydrofuran
Azole
Heteroaromatic compound
Imidazole
Secondary alcohol
Polyol
Secondary amine
Organoheterocyclic compound
Acetal
Azacycle
Oxacycle
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Alcohol
Primary alcohol
Amine
Organonitrogen compound
Organopnictogen compound
Organooxygen compound
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	-1.3	ALOGPS
logP	-3.5	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	12.02	ChemAxon
pKa (Strongest Basic)	3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	224.93 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	122 m³·mol⁻¹	ChemAxon
Polarizability	51.94 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	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

C00007550

Chemspider ID

9887971

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11713250

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,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0171902)

MOL for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0171902 ((2r,3r,4s,5s,6r)-2-{[(2e)-4-({9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)-2-methylbut-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)