NP-MRD: Showing NP-Card for (2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol (NP0330291)

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Record Information

Version

2.0

Created at

2022-09-12 15:29:38 UTC

Updated at

2022-09-12 15:29:39 UTC

NP-MRD ID

NP0330291

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol

Description

(2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol is found in Ecklonia radiata, Saccharina japonica, Sargassum lacerifolium, Sphaerotrichia divaricata and Tridacna maxima. Based on a literature review very few articles have been published on [(R)-2,3-Dihydroxypropyl]5-(dimethylarsinyl)-5-deoxy-beta-D-ribofuranoside.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 39  0  0  0  0  0  0  0  0999 V2000
   -4.0388   -1.6936   -1.3161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8858   -0.1498   -0.1074 As  0  0  0  0  0  5  0  0  0  0  0  0
   -5.3672    1.0912   -0.4873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0346   -0.6109    1.4648 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1806    0.7440   -0.4493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0042   -0.0159    0.1121 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1491    0.7084   -0.1883 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1669    0.1481    0.5863 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1746    1.0451    0.7906 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4321    0.7323    0.3981 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6279    0.5531   -1.0837 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8675   -0.4597   -1.6270 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0806    0.1804   -1.3230 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9652    1.1110   -0.8282 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5024   -0.1321    1.9232 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8908   -1.4269    2.3198 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9761   -0.0734    1.5993 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5377   -1.2628    2.0874 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0148   -2.0044   -1.6415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5099   -2.5692   -0.7892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6103   -1.4220   -2.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1283    2.0713   -0.0546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2665    0.7008    0.0702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5946    1.1359   -1.5733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1947    1.7890   -0.0959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0380    0.7849   -1.5495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9020   -1.0083   -0.3318 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5573   -0.7750    0.1386 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1933    1.4680    0.8052 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8022   -0.2445    0.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4213    1.5429   -1.5555 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3677   -1.3032   -1.6407 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2843   -0.7910   -0.8706 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1960    0.0779   -2.4297 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9617    1.9710   -1.3031 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7531    0.6219    2.6830 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6169   -2.0288    1.5603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4743    0.8189    2.0027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2525   -1.3248    3.0476 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  6  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  3 23  1  0
  3 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  6
  8 28  1  6
 10 29  1  0
 10 30  1  0
 11 31  1  6
 12 32  1  0
 13 33  1  0
 13 34  1  0
 14 35  1  0
 15 36  1  1
 16 37  1  0
 17 38  1  1
 18 39  1  0
M  END


  Mrv1652309122217292D          

 18 18  0  0  1  0            999 V2000
   -5.1062    0.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6213    1.2717    0.0000 As  0  0  0  0  0  0  0  0  0  0  0  0
   -3.9538    0.7867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2887    1.7566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1363    1.9391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3159    1.8529    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7638    2.4660    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0101    2.1304    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2957    2.5429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5812    2.1304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1333    2.5429    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1333    3.3679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8477    2.1304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5622    2.5429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0964    1.3099    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4833    0.7579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9034    1.1384    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2389    0.3847    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
  2  4  2  0  0  0  0
  2  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  8 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
  6 17  1  0  0  0  0
 17 18  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0330291

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[As](C)(=O)C[C@H]1O[C@@H](OC[C@H](O)CO)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H21AsO7/c1-11(2,16)3-7-8(14)9(15)10(18-7)17-5-6(13)4-12/h6-10,12-15H,3-5H2,1-2H3/t6-,7-,8-,9-,10-/m1/s1

> <INCHI_KEY>
GPGHDFGTUWSQOQ-VVULQXIFSA-N

> <FORMULA>
C10H21AsO7

> <MOLECULAR_WEIGHT>
328.193

> <EXACT_MASS>
328.050323

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
28.17193103596332

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S)-2-[(2R)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol

> <JCHEM_LOGP>
-2.617700000000002

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.485467132452989

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.274588900783849

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9682677554203307

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
57.5714

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S)-2-[(2R)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      -9.532   1.128   0.000  0.00  0.00           C+0
HETATM    2 As   UNK     0      -8.626   2.374   0.000  0.00  0.00          As+0
HETATM    3  C   UNK     0      -7.380   1.469   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -9.872   3.279   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -7.721   3.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.190   3.459   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.159   4.603   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -3.752   3.977   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.419   4.747   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.085   3.977   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.249   4.747   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.249   6.287   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.582   3.977   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.916   4.747   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -3.913   2.445   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.769   1.415   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -5.420   2.125   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -6.046   0.718   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7   17                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   15                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13                                                            
CONECT   15    8   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    6   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
[(R)-2,3-Dihydroxypropyl]5-(dimethylarsinyl)-5-deoxy-b-D-ribofuranoside	Generator
[(R)-2,3-Dihydroxypropyl]5-(dimethylarsinyl)-5-deoxy-β-D-ribofuranoside	Generator

Chemical Formula

C₁₀H₂₁AsO₇

Average Mass

328.1930 Da

Monoisotopic Mass

328.05032 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[As](C)(=O)C[C@H]1O[C@@H](OC[C@H](O)CO)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C10H21AsO7/c1-11(2,16)3-7-8(14)9(15)10(18-7)17-5-6(13)4-12/h6-10,12-15H,3-5H2,1-2H3/t6-,7-,8-,9-,10-/m1/s1

InChI Key

GPGHDFGTUWSQOQ-VVULQXIFSA-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
Ecklonia radiata	LOTUS Database	35616633
Saccharina japonica	LOTUS Database	35616633
Sargassum lacerifolium	LOTUS Database	35616633
Sphaerotrichia divaricata	LOTUS Database	35616633
Tridacna maxima	LOTUS Database	35616633

Chemical Taxonomy

Classification

Not classified

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

9373290

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11198221

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)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol (NP0330291)

MOL for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

3D MOL for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

3D SDF for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

3D-SDF for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

PDB for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

3D PDB for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

SMILES for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

INCHI for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

Structure for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)

3D Structure for NP0330291 ((2r,3r,4s,5s)-2-[(2r)-2,3-dihydroxypropoxy]-5-[(dimethylarsoryl)methyl]oxolane-3,4-diol)