NP-MRD: Showing NP-Card for [(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid (NP0252986)

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Record Information

Version

2.0

Created at

2022-09-07 16:42:29 UTC

Updated at

2022-09-07 16:42:29 UTC

NP-MRD ID

NP0252986

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid

Description

{[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)-5-(phosphonooxy)oxolan-2-yl]methoxy}phosphonic acid belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. [(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid is found in Arabidopsis thaliana. Based on a literature review very few articles have been published on {[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)-5-(phosphonooxy)oxolan-2-yl]methoxy}phosphonic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 34  0  0  0  0  0  0  0  0999 V2000
    4.7384    0.5274   -1.0655 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6111    0.1415    0.3912 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.3302    1.3198    1.3972 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3612   -1.3404    0.7126 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9896    0.0358    0.8407 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1495    0.6605   -0.0799 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7320    0.4952    0.4380 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2027    1.0516   -0.3509 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4052    0.3098   -0.2384 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8510    0.1349   -1.6927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9494   -0.6868   -2.3824 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2207    1.0905    0.4932 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7821    0.7770    0.7507 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.0924   -0.3952    1.6781 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4665    2.1347    1.5584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7452    0.5682   -0.6166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0388   -1.0255    0.2842 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7100   -1.4555    1.3959 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4305   -0.9601    0.6391 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2305   -1.7124   -0.1973 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5414    2.1460    0.8811 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7950   -2.0858    0.4317 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3829    1.7394   -0.1709 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2051    0.2136   -1.0896 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7102    0.9827    1.4440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8868   -0.2407   -1.7639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8364    1.1009   -2.2420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3408   -1.5116   -2.7095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4945    2.8559    0.8657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1283   -0.3434   -0.6760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1241   -1.8459   -0.4834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2963   -1.1743    2.2459 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6304   -1.2752    1.6820 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7332   -2.2325   -0.8521 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10  9  1  0
  9 12  1  1
 12 13  1  0
 13 15  1  0
 13 16  1  0
 13 14  2  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  2  1  0
  2  3  1  0
  2  4  1  0
  2  1  2  0
  7 19  1  0
 19 20  1  0
 19 17  1  0
 17 18  1  0
 17  9  1  0
 11 28  1  0
 10 26  1  0
 10 27  1  0
 15 29  1  0
 16 30  1  0
  7 25  1  1
  6 23  1  0
  6 24  1  0
  3 21  1  0
  4 22  1  0
 19 33  1  1
 20 34  1  0
 17 31  1  6
 18 32  1  0
M  END


  Mrv1652309072218422D          

 20 20  0  0  1  0            999 V2000
   -1.8213    0.7709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4857    0.0172    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2394   -0.3183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7320    0.3528    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7912    1.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8649    2.5120    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0802    2.2571    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6099    3.2966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6495    2.7669    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  1  0  0  0  0
  9 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 13 16  1  0  0  0  0
  9 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
  7 19  1  0  0  0  0
 19 20  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0252986

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@]1(OP(O)(O)=O)O[C@H](COP(O)(O)=O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H14O12P2/c7-2-6(18-20(13,14)15)5(9)4(8)3(17-6)1-16-19(10,11)12/h3-5,7-9H,1-2H2,(H2,10,11,12)(H2,13,14,15)/t3-,4+,5-,6-/m1/s1

> <INCHI_KEY>
YXWOAJXNVLXPMU-JGWLITMVSA-N

> <FORMULA>
C6H14O12P2

> <MOLECULAR_WEIGHT>
340.114

> <EXACT_MASS>
339.996049887

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
25.25547692269447

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,4R,5R)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxy}phosphonic acid

> <JCHEM_LOGP>
-3.0051313806666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.3703815262407373

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.6839676218192321

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4678657648404636

> <JCHEM_POLAR_SURFACE_AREA>
203.43999999999997

> <JCHEM_REFRACTIVITY>
58.10659999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,4R,5R)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0      -3.400   1.439   0.000  0.00  0.00           O+0
HETATM    2  P   UNK     0      -2.773   0.032   0.000  0.00  0.00           P+0
HETATM    3  O   UNK     0      -4.180  -0.594   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -1.366   0.659   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -2.147  -1.375   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.029   3.224   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.477   2.904   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.090   3.224   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       1.614   4.689   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0       0.150   4.213   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.139   6.154   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.079   5.165   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.735  -1.536   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                                                       
CONECT    7    6    8   19                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   12   17                                             
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13                                                            
CONECT   17    9   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    7   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Value	Source
{[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)-5-(phosphonooxy)oxolan-2-yl]methoxy}phosphonate	Generator

Chemical Formula

C₆H₁₄O₁₂P₂

Average Mass

340.1140 Da

Monoisotopic Mass

339.99605 Da

IUPAC Name

{[(2R,3R,4R,5R)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxy}phosphonic acid

Traditional Name

[(2R,3R,4R,5R)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

OC[C@]1(OP(O)(O)=O)O[C@H](COP(O)(O)=O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C6H14O12P2/c7-2-6(18-20(13,14)15)5(9)4(8)3(17-6)1-16-19(10,11)12/h3-5,7-9H,1-2H2,(H2,10,11,12)(H2,13,14,15)/t3-,4+,5-,6-/m1/s1

InChI Key

YXWOAJXNVLXPMU-JGWLITMVSA-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 pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose-5-phosphate
Pentose phosphate
Glycosyl compound
C-glycosyl compound
Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-3	ChemAxon
pKa (Strongest Acidic)	0.68	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	203.44 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	58.11 m³·mol⁻¹	ChemAxon
Polarizability	25.26 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

162979383

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)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid (NP0252986)

MOL for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

3D MOL for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

3D SDF for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

3D-SDF for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

PDB for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

3D PDB for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

SMILES for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

INCHI for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

Structure for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)

3D Structure for NP0252986 ([(2r,3r,4r,5r)-3,4-dihydroxy-2-(hydroxymethyl)-5-[(phosphonooxy)methyl]oxolan-2-yl]oxyphosphonic acid)