NP-MRD: Showing NP-Card for Uridine 2',3'-cyclic phosphate (NP0091524)

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Record Information

Version

2.0

Created at

2022-05-11 18:40:27 UTC

Updated at

2022-05-11 18:40:27 UTC

NP-MRD ID

NP0091524

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Uridine 2',3'-cyclic phosphate

Description

Uridine 2',3'-cyclic phosphate, also known as CUMP, belongs to the class of organic compounds known as 2',3'-cyclic pyrimidine nucleotides. These are pyrimidine nucleotides in which the oxygen atoms linked to the C2 and C3 carbon atoms of the ribose moiety are both bonded the same phosphorus atom of the phosphate group. Uridine 2',3'-cyclic phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Uridine 2',3'-cyclic phosphate is found in Apis cerana. Uridine 2',3'-cyclic phosphate exists in all living organisms, ranging from bacteria to humans.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 33  0  0  0  0  0  0  0  0999 V2000
    5.5182    0.1547    0.5312 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2852    0.0252    0.2957 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7429    0.6581   -0.8038 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3998    0.4925   -1.0249 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6144   -0.2649   -0.2005 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2289   -0.3385   -0.5710 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1298    0.9627   -0.9985 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4920    1.0407   -1.0051 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0039    2.4402   -0.7104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6088    2.9094    0.5182 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9578    0.1418    0.1176 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.9384   -0.6954   -0.3370 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6861   -2.0536    0.6428 P   0  0  1  0  0  5  0  0  0  0  0  0
   -3.3854   -1.9034    1.9725 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1036   -3.4792   -0.1480 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0112   -1.8856    0.8162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7399   -0.5811    0.5174 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1737   -0.8599    0.8501 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4608   -1.5534    1.6068 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5036   -0.7178    1.1006 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3819    1.2506   -1.4402 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9844    0.9970   -1.8955 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0686   -1.0048   -1.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8720    0.7381   -1.9929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6498    3.1676   -1.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1144    2.3947   -0.8285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2230    2.7436    1.2543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3827    0.7303    0.9658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6385   -4.2186    0.3162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3407   -0.0861    1.4499 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9156   -1.2047    1.9448 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 16  1  0
 16 13  1  0
 13 15  1  6
 13 14  2  0
 13 12  1  0
 12 11  1  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  2 20  1  0
 20 18  1  0
 18 19  2  0
 11  8  1  0
 18  5  1  0
 11 17  1  0
 10 27  1  0
  9 25  1  0
  9 26  1  0
  8 24  1  6
  6 23  1  6
 17 30  1  1
 15 29  1  0
 11 28  1  1
  4 22  1  0
  3 21  1  0
 20 31  1  0
M  END


  Mrv0541 02241201482D          

 20 22  0  0  1  0            999 V2000
    7.3786  -10.0062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.0460   -9.5213    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6335  -10.7908    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7134  -10.0062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4585  -10.7908    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.5518   -9.6330    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.0443   -8.9294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9758   -9.7516    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.3665   -8.4591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2296  -10.1034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6203   -8.8108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1611  -10.9255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7905   -8.5777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5939   -9.7513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4224   -8.9443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7134  -11.5755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0460  -12.0604    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    7.6335  -12.7749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4585  -12.7749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3786  -11.5755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  4  6  1  1  0  0  0
  8  7  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  2  0  0  0  0
  6 10  1  0  0  0  0
  6 11  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  2  0  0  0  0
  1 14  1  1  0  0  0
 15 14  1  0  0  0  0
  5 16  1  6  0  0  0
 18 17  2  0  0  0  0
 19 17  1  0  0  0  0
 20 17  1  0  0  0  0
 16 17  1  0  0  0  0
  3 20  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0091524

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H11N2O8P/c12-3-4-6-7(19-20(15,16)18-6)8(17-4)11-2-1-5(13)10-9(11)14/h1-2,4,6-8,12H,3H2,(H,15,16)(H,10,13,14)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
HWDMHJDYMFRXOX-XVFCMESISA-N

> <FORMULA>
C9H11N2O8P

> <MOLECULAR_WEIGHT>
306.166

> <EXACT_MASS>
306.02530185

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
24.699985437895975

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2H-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.30

> <JCHEM_LOGP>
-1.6422703816666666

> <ALOGPS_LOGS>
-1.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.701346058916792

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7621871169083843

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9813280853111124

> <JCHEM_POLAR_SURFACE_AREA>
134.63000000000002

> <JCHEM_REFRACTIVITY>
59.6595

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2',3'-cyclic ump

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      13.773 -18.678   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      15.019 -17.773   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      14.249 -20.143   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.265 -18.678   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.789 -20.143   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      17.830 -17.982   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      20.616 -16.668   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      20.488 -18.203   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      19.351 -15.790   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.095 -18.860   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.958 -16.447   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      18.967 -20.394   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      22.009 -16.012   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      12.309 -18.202   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      11.988 -16.696   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      16.265 -21.608   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      15.019 -22.513   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      14.249 -23.846   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      15.789 -23.846   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      13.773 -21.608   0.000  0.00  0.00           O+0
CONECT    1    2    3   14                                                  
CONECT    2    1    4                                                       
CONECT    3    1    5   20                                                  
CONECT    4    2    5    6                                                  
CONECT    5    3    4   16                                                  
CONECT    6    4   10   11                                                  
CONECT    7    8    9   13                                                  
CONECT    8    7   10                                                       
CONECT    9    7   11                                                       
CONECT   10    8    6   12                                                  
CONECT   11    9    6                                                       
CONECT   12   10                                                            
CONECT   13    7                                                            
CONECT   14    1   15                                                       
CONECT   15   14                                                            
CONECT   16    5   17                                                       
CONECT   17   18   19   20   16                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17    3                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Value	Source
CUMP	ChEBI
Uridine 2',3'-cyclophosphate	ChEBI
Uridine, cyclic 2',3'-(hydrogen phosphate)	ChEBI
Uridine 2',3'-cyclophosphoric acid	Generator
Uridine, cyclic 2',3'-(hydrogen phosphoric acid)	Generator
Uridine 2',3'-cyclic phosphoric acid	Generator
1-(2,3-O-Phosphinico-a-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2,3-O-Phosphinico-alpha-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
2',3'-CUMP	HMDB
Uridine 2',3'-cyclic monophosphate	HMDB
Uridine 2',3'-cyclophosphate, monosodium salt	MeSH

Chemical Formula

C₉H₁₁N₂O₈P

Average Mass

306.1660 Da

Monoisotopic Mass

306.02530 Da

IUPAC Name

1-[(3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2H-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

2',3'-cyclic ump

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C9H11N2O8P/c12-3-4-6-7(19-20(15,16)18-6)8(17-4)11-2-1-5(13)10-9(11)14/h1-2,4,6-8,12H,3H2,(H,15,16)(H,10,13,14)/t4-,6-,7-,8-/m1/s1

InChI Key

HWDMHJDYMFRXOX-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Apis cerana	LOTUS Database	35616633
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2',3'-cyclic pyrimidine nucleotides. These are pyrimidine nucleotides in which the oxygen atoms linked to the C2 and C3 carbon atoms of the ribose moiety are both bonded the same phosphorus atom of the phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Cyclic pyrimidine nucleotides

Direct Parent

2',3'-cyclic pyrimidine nucleotides

Alternative Parents

Substituents

2',3'-cyclic pyrimidine ribonucleotide
Ribonucleoside 3'-phosphate
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Pyrimidine
1,3_dioxaphospholane
Heteroaromatic compound
Tetrahydrofuran
Vinylogous amide
Urea
Lactam
Organoheterocyclic compound
Azacycle
Oxacycle
Alcohol
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

2',3'-cyclic pyrimidine nucleotide (CHEBI:28637 )
2',3'-Cyclic nucleotides (C02355 )

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	-1.3	ALOGPS
logP	-1.6	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.76	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	134.63 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	59.66 m³·mol⁻¹	ChemAxon
Polarizability	24.7 Å³	ChemAxon
Number of Rings	3	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

HMDB0011640

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB028337

KNApSAcK ID

Not Available

Chemspider ID

388781

KEGG Compound ID

C02355

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439715

PDB ID

Not Available

ChEBI ID

28637

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Uridine 2',3'-cyclic phosphate (NP0091524)

MOL for NP0091524 (Uridine 2',3'-cyclic phosphate)

3D MOL for NP0091524 (Uridine 2',3'-cyclic phosphate)

3D SDF for NP0091524 (Uridine 2',3'-cyclic phosphate)

3D-SDF for NP0091524 (Uridine 2',3'-cyclic phosphate)

PDB for NP0091524 (Uridine 2',3'-cyclic phosphate)

3D PDB for NP0091524 (Uridine 2',3'-cyclic phosphate)

SMILES for NP0091524 (Uridine 2',3'-cyclic phosphate)

INCHI for NP0091524 (Uridine 2',3'-cyclic phosphate)

Structure for NP0091524 (Uridine 2',3'-cyclic phosphate)

3D Structure for NP0091524 (Uridine 2',3'-cyclic phosphate)