NP-MRD: Showing NP-Card for (4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one (NP0225104)

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Record Information

Version

2.0

Created at

2022-09-06 03:43:49 UTC

Updated at

2022-09-06 03:43:49 UTC

NP-MRD ID

NP0225104

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one

Description

3',5'-Cyclic CMP, also known as CCMP or cyclic CMP, 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. 3',5'-Cyclic CMP is an extremely weak basic (essentially neutral) compound (based on its pKa). 3',5'-Cyclic CMP may be a unique S. (4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one is found in Pisum sativum. (4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one was first documented in 2014 (PMID: 25017019). Cerevisiae (yeast) metabolite (PMID: 25062586).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222192D          

 20 22  0  0  1  0            999 V2000
    0.0000   -0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -1.3100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6675   -1.3100    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.0946    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -2.0946    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4521   -1.0550    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4290    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8974   -2.7620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5618   -3.5157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8975   -2.7620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4246   -4.4416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4246   -3.6166    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2620   -3.6604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  1  6  0  0  0
  5 10  1  0  0  0  0
  5 11  2  0  0  0  0
  6 12  2  0  0  0  0
  7 15  1  1  0  0  0
  8 17  1  6  0  0  0
 10 13  2  0  0  0  0
 13 14  1  0  0  0  0
  7  8  1  0  0  0  0
 12 13  1  0  0  0  0
 15 16  1  0  0  0  0
 16 19  1  0  0  0  0
 17 19  1  0  0  0  0
 19 18  2  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0225104

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC(=O)N(C=C1)[C@@H]1O[C@@H]2COP(O)(=O)O[C@H]2[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N3O7P/c10-5-1-2-12(9(14)11-5)8-6(13)7-4(18-8)3-17-20(15,16)19-7/h1-2,4,6-8,13H,3H2,(H,15,16)(H2,10,11,14)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
WCPTXJJVVDAEMW-XVFCMESISA-N

> <FORMULA>
C9H12N3O7P

> <MOLECULAR_WEIGHT>
305.1812

> <EXACT_MASS>
305.041286265

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
25.36888565838693

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxo-hexahydro-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-4-amino-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.89

> <JCHEM_LOGP>
-2.25419340445604

> <ALOGPS_LOGS>
-1.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.729086225684568

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8343285823320992

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6296197752249911

> <JCHEM_POLAR_SURFACE_AREA>
143.91

> <JCHEM_REFRACTIVITY>
61.6387

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.23e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cCMP

> <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       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0      -1.246  -2.445   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.246  -2.445   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.770  -3.910   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.770  -3.910   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.711  -1.969   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   3.080   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       0.000   4.620   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -1.675  -5.156   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.049  -6.563   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.675  -5.156   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.793  -8.291   0.000  0.00  0.00           O+0
HETATM   19  P   UNK     0       0.793  -6.751   0.000  0.00  0.00           P+0
HETATM   20  O   UNK     0       2.356  -6.833   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2   10   11                                                  
CONECT    6    2   12                                                       
CONECT    7    3   15    8                                                  
CONECT    8    4   17    7                                                  
CONECT    9    4                                                            
CONECT   10    5   13                                                       
CONECT   11    5                                                            
CONECT   12    6   13                                                       
CONECT   13   10   14   12                                                  
CONECT   14   13                                                            
CONECT   15    7   16                                                       
CONECT   16   15   19                                                       
CONECT   17    8   19                                                       
CONECT   18   19                                                            
CONECT   19   16   17   18   20                                             
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Value	Source
CCMP	ChEBI
Cyclic CMP	ChEBI
Cytidine 3',5'-cyclic monophosphate	ChEBI
Cytidine, cyclic 3',5'-(hydrogen phosphate)	ChEBI
Cytidine 3',5'-cyclic monophosphoric acid	Generator
Cytidine, cyclic 3',5'-(hydrogen phosphoric acid)	Generator
Cyclic monophosphate, cytidine	MeSH
Cytidine cyclic monophosphate	MeSH
Cytidine cyclic-3',5'-monophosphate	MeSH
monoPhosphate, cytidine cyclic	MeSH
Cyclic-3',5'-monophosphate, cytidine	MeSH
Cytidine cyclic 3,5 monophosphate	MeSH
CMP, Cyclic	MeSH
Cyclic CMP, monosodium salt	MeSH
Cytidine cyclic 3',5' monophosphate	MeSH

Chemical Formula

C₉H₁₂N₃O₇P

Average Mass

305.1812 Da

Monoisotopic Mass

305.04129 Da

IUPAC Name

1-[(4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxo-hexahydro-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-4-amino-1,2-dihydropyrimidin-2-one

Traditional Name

cCMP

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@@H]2COP(O)(=O)O[C@H]2[C@H]1O

InChI Identifier

InChI=1S/C9H12N3O7P/c10-5-1-2-12(9(14)11-5)8-6(13)7-4(18-8)3-17-20(15,16)19-7/h1-2,4,6-8,13H,3H2,(H,15,16)(H2,10,11,14)/t4-,6-,7-,8-/m1/s1

InChI Key

WCPTXJJVVDAEMW-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
Pisum sativum	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 phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Hydroxypyrimidine
Hydropyrimidine
Organic phosphoric acid derivative
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

3',5'-cyclic pyrimidine nucleotide (CHEBI:17065 )
3',5'-Cyclic nuclcleotides (C00941 )

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	-1.9	ALOGPS
logP	-2.3	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.83	ChemAxon
pKa (Strongest Basic)	-0.63	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	143.91 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	61.64 m³·mol⁻¹	ChemAxon
Polarizability	25.37 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

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

C00941

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

19236

PDB ID

Not Available

ChEBI ID

17065

Good Scents ID

Not Available

References

General References

Laue S, Winterhoff M, Kaever V, van den Heuvel JJ, Russel FG, Seifert R: cCMP is a substrate for MRP5. Naunyn Schmiedebergs Arch Pharmacol. 2014 Sep;387(9):893-5. doi: 10.1007/s00210-014-1018-9. Epub 2014 Jul 15. [PubMed:25017019 ]
Hartwig C, Bahre H, Wolter S, Beckert U, Kaever V, Seifert R: cAMP, cGMP, cCMP and cUMP concentrations across the tree of life: High cCMP and cUMP levels in astrocytes. Neurosci Lett. 2014 Sep 5;579:183-7. doi: 10.1016/j.neulet.2014.07.019. Epub 2014 Jul 23. [PubMed:25062586 ]
LOTUS database [Link]

Showing NP-Card for (4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one (NP0225104)

MOL for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

3D MOL for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

3D SDF for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

3D-SDF for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

PDB for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

3D PDB for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

SMILES for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

INCHI for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

Structure for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)

3D Structure for NP0225104 ((4ar,6r,7r,7as)-2,7-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)-tetrahydro-4h-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one)