NP-MRD: Showing NP-Card for 2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol (NP0320044)

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Record Information

Version

2.0

Created at

2022-09-11 21:24:24 UTC

Updated at

2022-09-11 21:24:25 UTC

NP-MRD ID

NP0320044

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol

Description

2-[(6-Hydroxy-9H-purin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol belongs to the class of organic compounds known as thioglycosides. These are glycoside in which a sugar group is bonded through one carbon to another group via a S-glycosidic bond. Based on a literature review very few articles have been published on 2-[(6-hydroxy-9H-purin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 36  0  0  0  0  0  0  0  0999 V2000
    4.8657    0.4945   -1.8466 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5131    1.3752   -1.0162 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.2081    0.1731   -0.6759 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1158    0.7565   -0.0341 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4877   -0.3256    0.5137 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7105   -0.0641    1.3262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7988    0.5799    0.6875 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1104    1.8843    0.5507 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2549    2.0134   -0.1435 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6733    0.7703   -0.4503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7747    0.3319   -1.1416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6830    1.2328   -1.6597 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9664   -0.9751   -1.3125 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0862   -1.8457   -0.8103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0001   -1.4427   -0.1299 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7812   -0.1169    0.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6193   -0.9818    1.2795 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0198   -0.1462    2.3248 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7050   -0.9360    0.1959 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9537   -0.7034    0.7451 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8469    0.7290   -1.3636 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7450   -0.6130   -1.7635 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8611    0.7156   -2.9310 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8532   -0.1999   -1.6768 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2474   -1.0330   -0.3322 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4045    0.5820    2.2018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0552   -1.0116    1.7854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5187    2.6991    0.9459 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8837    2.0557   -1.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2055   -2.9331   -0.9279 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3940   -1.9954    1.6022 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8924    0.7986    2.1034 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6902   -1.8724   -0.3612 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8888    0.0040    1.4308 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  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
  5 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19  3  1  0
 16  7  1  0
 16 10  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  6
  5 25  1  6
  6 26  1  0
  6 27  1  0
  8 28  1  0
 12 29  1  0
 14 30  1  0
 17 31  1  1
 18 32  1  0
 19 33  1  6
 20 34  1  0
M  END


  Mrv1652309112223242D          

 20 22  0  0  0  0            999 V2000
   -2.6719   -2.3314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0044   -1.8464    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2508   -2.1820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363   -1.7695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  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 O   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
    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
   -0.2587   -3.0752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1538   -3.7897    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0792   -2.9890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6313   -3.6021    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  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
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 10 16  1  0  0  0  0
  7 16  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
  3 19  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0320044

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CSC1OC(CN2C=NC3=C(O)N=CN=C23)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N4O4S/c1-20-11-8(17)7(16)5(19-11)2-15-4-14-6-9(15)12-3-13-10(6)18/h3-5,7-8,11,16-17H,2H2,1H3,(H,12,13,18)

> <INCHI_KEY>
KHOAKFWUEHUJTA-UHFFFAOYSA-N

> <FORMULA>
C11H14N4O4S

> <MOLECULAR_WEIGHT>
298.32

> <EXACT_MASS>
298.073576121

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
28.140994916794174

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(6-hydroxy-9H-purin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol

> <JCHEM_LOGP>
-0.21148552500000006

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.678109454786576

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.663694540832992

> <JCHEM_PKA_STRONGEST_BASIC>
0.12006055485512512

> <JCHEM_POLAR_SURFACE_AREA>
113.52000000000001

> <JCHEM_REFRACTIVITY>
71.34749999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.987  -4.352   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0      -3.742  -3.447   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0      -2.335  -4.073   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.001  -3.303   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.924   1.777   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       6.258  -0.533   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       4.924  -2.843   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.483  -5.740   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.287  -7.074   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -2.015  -5.579   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -3.045  -6.724   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   16                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   10    7                                                  
CONECT   17    5   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    3   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Value	Source
2-[(6-Hydroxy-9H-purin-9-yl)methyl]-5-(methylsulphanyl)oxolane-3,4-diol	Generator

Chemical Formula

C₁₁H₁₄N₄O₄S

Average Mass

298.3200 Da

Monoisotopic Mass

298.07358 Da

IUPAC Name

2-[(6-hydroxy-9H-purin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol

Traditional Name

2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

CSC1OC(CN2C=NC3=C(O)N=CN=C23)C(O)C1O

InChI Identifier

InChI=1S/C11H14N4O4S/c1-20-11-8(17)7(16)5(19-11)2-15-4-14-6-9(15)12-3-13-10(6)18/h3-5,7-8,11,16-17H,2H2,1H3,(H,12,13,18)

InChI Key

KHOAKFWUEHUJTA-UHFFFAOYSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thioglycosides. These are glycoside in which a sugar group is bonded through one carbon to another group via a S-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Thioglycosides

Alternative Parents

Substituents

S-glycosyl compound
Hypoxanthine
Pentose monosaccharide
Imidazopyrimidine
Purine
Hydroxypyrimidine
Monosaccharide
N-substituted imidazole
Pyrimidine
Heteroaromatic compound
Azole
Imidazole
Monothioacetal
Tetrahydrofuran
1,2-diol
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Sulfenyl compound
Organopnictogen compound
Organosulfur compound
Organonitrogen compound
Hydrocarbon derivative
Alcohol
Organic nitrogen 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	-0.21	ChemAxon
pKa (Strongest Acidic)	11.66	ChemAxon
pKa (Strongest Basic)	0.12	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.52 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	71.35 m³·mol⁻¹	ChemAxon
Polarizability	28.14 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

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

162855820

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-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol (NP0320044)

MOL for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

3D MOL for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

3D SDF for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

3D-SDF for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

PDB for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

3D PDB for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

SMILES for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

INCHI for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

Structure for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)

3D Structure for NP0320044 (2-[(6-hydroxypurin-9-yl)methyl]-5-(methylsulfanyl)oxolane-3,4-diol)