NP-MRD: Showing NP-Card for [(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid (NP0273902)

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Record Information

Version

2.0

Created at

2022-09-08 21:05:49 UTC

Updated at

2022-09-08 21:05:49 UTC

NP-MRD ID

NP0273902

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid

Description

ZINC3870260 belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety. [(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid is found in Arabidopsis thaliana. Based on a literature review very few articles have been published on ZINC3870260.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 35  0  0  0  0  0  0  0  0999 V2000
    1.4451    2.3921   -0.0585 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2808    1.4571    0.0099 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4044    1.6934    0.7113 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3659    0.7465    0.8426 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5227    1.0132    1.5743 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1585   -0.4571    0.2397 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9944   -0.6609   -0.4703 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0409    0.2691   -0.6041 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8226    0.1274   -1.3186 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1565    0.8547   -0.5973 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5907    0.0422    0.4244 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1039    0.0166    0.3861 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6357    1.2972    0.5530 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3082    1.3009    0.5151 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.7653    1.4166   -0.9263 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8975   -0.1392    1.1893 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9508    2.5993    1.4009 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1108   -1.3700    0.1552 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0793   -2.3146    0.4244 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1916   -1.2254   -1.3126 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8349   -2.2357   -1.9065 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3811    1.2727    1.1058 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8930   -1.2664    0.3048 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8489   -1.6023   -0.9333 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8797    0.5648   -2.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2950    0.3965    1.4291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4880   -0.4010   -0.5739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5191   -0.6414    1.1840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8191   -0.2767    0.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1354    3.3496    0.7537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8143   -1.5119    0.7480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4394   -2.7200   -0.4099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8128   -1.0991   -1.8152 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2288   -2.8884   -2.3233 H   0  0  0  0  0  0  0  0  0  0  0  0
 19 18  1  0
 18 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 16  1  0
 14 17  1  0
 14 15  2  0
 11 10  1  0
 10  9  1  0
  9 20  1  0
 20 21  1  0
  9  8  1  0
  8  7  1  0
  7  6  2  0
  6  4  1  0
  4  5  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
 20 18  1  0
  2  8  1  0
 19 32  1  0
 18 31  1  1
 11 26  1  1
 12 27  1  0
 12 28  1  0
 16 29  1  0
 17 30  1  0
  9 25  1  6
 20 33  1  6
 21 34  1  0
  7 24  1  0
  6 23  1  0
  5 22  1  0
M  END


  Mrv1652309082223052D          

 21 22  0  0  1  0            999 V2000
    1.3222    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    2.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    2.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    3.2384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6486   -1.9986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3130   -2.7523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7980   -3.4197    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.2829   -4.0871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1305   -3.9046    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4654   -2.9348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  9  8  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 14 17  1  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
  9 20  1  0  0  0  0
 20 21  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0273902

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@H](COP(O)(O)=O)O[C@H]([C@H]1O)N1C=CC(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6+,7-,8+/m0/s1

> <INCHI_KEY>
DJJCXFVJDGTHFX-VXUIKNBNSA-N

> <FORMULA>
C9H13N2O9P

> <MOLECULAR_WEIGHT>
324.182

> <EXACT_MASS>
324.035867005

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.598308846897773

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2S,3S,4S,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid

> <JCHEM_LOGP>
-2.1713073686666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.231842033035198

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2255015374573275

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6645541134946784

> <JCHEM_POLAR_SURFACE_AREA>
169.35

> <JCHEM_REFRACTIVITY>
63.7602

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(2S,3S,4S,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid

> <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  O   UNK     0       2.468   1.425   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.802   2.195   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       3.802   3.735   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       5.136   4.505   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.136   6.045   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.469   3.735   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.469   2.195   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       5.136   1.425   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.381  -1.020   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.906  -2.485   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.811  -3.731   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.184  -5.138   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       7.090  -6.383   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0       7.995  -7.629   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       5.844  -7.289   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       8.335  -5.478   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.460  -3.731   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    2    9                                                  
CONECT    9    8   10   20                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14                                                            
CONECT   18   11   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18    9   21                                                  
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₃N₂O₉P

Average Mass

324.1820 Da

Monoisotopic Mass

324.03587 Da

IUPAC Name

{[(2S,3S,4S,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid

Traditional Name

[(2S,3S,4S,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@H](COP(O)(O)=O)O[C@H]([C@H]1O)N1C=CC(O)=NC1=O

InChI Identifier

InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6+,7-,8+/m0/s1

InChI Key

DJJCXFVJDGTHFX-VXUIKNBNSA-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 pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Vinylogous amide
Heteroaromatic compound
Oxolane
1,2-diol
Urea
Secondary alcohol
Lactam
Azacycle
Oxacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxide
Alcohol
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-2.2	ChemAxon
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	169.35 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	63.76 m³·mol⁻¹	ChemAxon
Polarizability	26.6 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

40467906

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid (NP0273902)

MOL for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

3D MOL for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

3D SDF for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

3D-SDF for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

PDB for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

3D PDB for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

SMILES for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

INCHI for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

Structure for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)

3D Structure for NP0273902 ([(2s,3s,4s,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid)