NP-MRD: Showing NP-Card for disodium salt 3'-uridylic acid (NP0200622)

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Record Information

Version

2.0

Created at

2022-09-04 19:30:20 UTC

Updated at

2022-09-04 19:30:20 UTC

NP-MRD ID

NP0200622

Secondary Accession Numbers

None

Natural Product Identification

Common Name

disodium salt 3'-uridylic acid

Description

Uridine 3'-monophosphate, also known as uridine 3'-phosphoric acid or 3'-uridylic acid, belongs to the class of organic compounds known as ribonucleoside 3'-phosphates. These are ribonucleosides that contain a phosphate group attached to the C-3 carbon of the ribose or deoxyribose moiety. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. Uridine 3'-monophosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Uridine 3'-monophosphate exists in all living organisms, ranging from bacteria to humans. disodium salt 3'-uridylic acid is found in Daphnia pulex. A pyrimidine ribonucleoside 3'-monophosphate having uracil as the nucleobase.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 35  0  0  0  0  0  0  0  0999 V2000
    5.5854   -1.7882    0.2940 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5020   -1.1731    0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3260   -1.8580    0.2912 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1249   -1.1993    0.0979 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1180    0.0984   -0.2600 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8587    0.7881   -0.4625 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2827    1.1784    0.7405 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0551    1.3643    0.3999 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9223    1.6243    1.5979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4453    2.7805    2.2153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3700    0.0404   -0.2711 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5091    0.0744   -1.0320 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5577   -1.2077   -0.7338 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.9062   -0.8337   -1.3246 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0535   -2.6242   -1.5073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7556   -1.5378    0.8905 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1465   -0.0548   -1.1924 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5097    0.6278   -2.3630 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3018    0.7357   -0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3295    1.9524   -0.7594 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4873    0.1267   -0.2447 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2937   -2.8885    0.5751 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2050   -1.7532    0.2416 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0936    1.7394   -1.0194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1307    2.1544   -0.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9792    1.7194    1.3732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7624    0.7881    2.3150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5091    3.5167    1.5680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3040   -0.8129    0.4203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3947   -3.4312   -1.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6053   -1.2072    1.2449 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1597   -1.0810   -1.3763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1537    1.5503   -2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4014    0.5908   -0.3638 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6 17  1  0
 17 18  1  0
 17 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 16  1  0
 13 14  2  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  2 21  1  0
 21 19  1  0
 19 20  2  0
 11  8  1  0
 19  5  1  0
 10 28  1  0
  9 26  1  0
  9 27  1  0
  8 25  1  6
  6 24  1  6
 17 32  1  6
 18 33  1  0
 11 29  1  1
 15 30  1  0
 16 31  1  0
  4 23  1  0
  3 22  1  0
 21 34  1  0
M  END

 
  Mrv1652309191919292D          

 21 22  0  0  0  0            999 V2000
   13.2753  -10.1145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8988   -9.5709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6788   -9.8331    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.9246  -10.6246    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.3805  -11.2466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7508  -10.6322    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.2240  -11.3060    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0130   -9.8522    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.3525   -9.3598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8006   -9.6063    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4098  -10.1689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2270  -10.9734    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.1972   -9.9228    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.3800   -9.1181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7708   -8.5557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9833   -8.8016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6457  -12.0252    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   14.9018  -12.8051    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4257  -11.7643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8661  -12.2879    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1656   -8.8744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  8 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  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
  5 17  1  0  0  0  0
  1  2  1  0  0  0  0
 17 18  1  0  0  0  0
  3  2  1  1  0  0  0
 17 19  2  0  0  0  0
  3  4  1  0  0  0  0
 17 20  1  0  0  0  0
  4  5  1  6  0  0  0
 14 21  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0200622

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N2O9P/c12-3-4-7(20-21(16,17)18)6(14)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
FOGRQMPFHUHIGU-XVFCMESISA-N

> <FORMULA>
C9H13N2O9P

> <MOLECULAR_WEIGHT>
324.1813

> <EXACT_MASS>
324.035866536

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.55651888785477

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.75

> <JCHEM_LOGP>
-2.1713073686666666

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.894408374166111

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8747321923263796

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9813008545882633

> <JCHEM_POLAR_SURFACE_AREA>
169.35

> <JCHEM_REFRACTIVITY>
63.7602

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.29e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
disodium salt 3'-uridylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-SEP-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-SEP-19         0                                  
HETATM    1  O   UNK     0      24.781 -18.880   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      25.944 -17.866   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.400 -18.355   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.859 -19.833   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      26.844 -20.994   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      29.402 -19.847   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      30.285 -21.105   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      29.891 -18.391   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      28.658 -17.472   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      31.361 -17.932   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      32.498 -18.982   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      32.157 -20.484   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0      33.968 -18.523   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      34.309 -17.020   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      33.172 -15.971   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      31.702 -16.430   0.000  0.00  0.00           C+0
HETATM   17  P   UNK     0      27.339 -22.447   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      27.817 -23.903   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      28.795 -21.960   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      25.883 -22.937   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      35.776 -16.566   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    9    2    4                                                  
CONECT    4    6    3    5                                                  
CONECT    5   17    4                                                       
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8    3                                                       
CONECT   10    8   11   16                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15   14   16                                                       
CONECT   16   15   10                                                       
CONECT   17    5   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17                                                            
CONECT   21   14                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Value	Source
Uridine 3'-phosphate	ChEBI
Uridine 3'-phosphoric acid	Generator
Uridine 3'-monophosphoric acid	Generator
3'-Uridylic acid	HMDB
3'-UMP	HMDB
3’-UMP	HMDB
Uridine 3'-(dihydrogen phosphate)	HMDB
Uridine 3’-(dihydrogen phosphate)	HMDB
Uridine 3’-monophosphate	HMDB
Uridine 3’-phosphate	HMDB
Uridine 3’-phosphoric acid	HMDB
Uridine 3'-monophosphate	ChEBI, KEGG

Chemical Formula

C₉H₁₃N₂O₉P

Average Mass

324.1813 Da

Monoisotopic Mass

324.03587 Da

IUPAC Name

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

Traditional Name

disodium salt 3'-uridylic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H13N2O9P/c12-3-4-7(20-21(16,17)18)6(14)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChI Key

FOGRQMPFHUHIGU-XVFCMESISA-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
Daphnia pulex	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ribonucleoside 3'-phosphates. These are ribonucleosides that contain a phosphate group attached to the C-3 carbon of the ribose or deoxyribose moiety. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Ribonucleoside 3'-phosphates

Sub Class

Not Available

Direct Parent

Ribonucleoside 3'-phosphates

Alternative Parents

Substituents

Ribonucleoside 3'-phosphate
Pentose phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Hydroxypyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Azacycle
Alcohol
Primary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organopnictogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine ribonucleoside 3'-monophosphate (CHEBI:28895 )
uridine phosphate (CHEBI:28895 )

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	-1.8	ALOGPS
logP	-2.2	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	0.87	ChemAxon
pKa (Strongest Basic)	-3	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	26.56 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

HMDB0060282

DrugBank ID

DB02714

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

91753

KEGG Compound ID

C01368

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101543

PDB ID

Not Available

ChEBI ID

28895

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for disodium salt 3'-uridylic acid (NP0200622)

MOL for NP0200622 (disodium salt 3'-uridylic acid)

3D MOL for NP0200622 (disodium salt 3'-uridylic acid)

3D SDF for NP0200622 (disodium salt 3'-uridylic acid)

3D-SDF for NP0200622 (disodium salt 3'-uridylic acid)

PDB for NP0200622 (disodium salt 3'-uridylic acid)

3D PDB for NP0200622 (disodium salt 3'-uridylic acid)

SMILES for NP0200622 (disodium salt 3'-uridylic acid)

INCHI for NP0200622 (disodium salt 3'-uridylic acid)

Structure for NP0200622 (disodium salt 3'-uridylic acid)

3D Structure for NP0200622 (disodium salt 3'-uridylic acid)