MiMeDB: Showing metabocard for 3',5'-cyclic CMP (MMDBc0057083)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-07-26 19:02:39 UTC

Update Date

2025-10-07 16:09:48 UTC

Metabolite ID

MMDBc0057083

Metabolite Identification

Common Name

3',5'-cyclic CMP

Description

3',5'-cyclic CMP is a cyclic nucleotide belonging to the class of pyrimidine nucleotides. Its chemical structure features a cyclic phosphate group linked to a cytidine base, which is essential in various biochemical pathways. This compound has garnered attention for its potential roles in nonenzymatic processes, particularly in the context of RNA synthesis. Notably, 3',5'-cyclic CMP can undergo nonenzymatic di- and trimerization at 20 °C under dry conditions when exposed to proton or UV irradiation, suggesting a pathway for the spontaneous generation of RNA (PMID:28471098 ). This oligomerization process indicates that pyrimidines, like purines, may have contributed to the origins of RNA under plausible prebiotic conditions, as well as in extraterrestrial environments (PMID:28471098 ). The ability of 3',5'-cyclic CMP to participate in such reactions highlights its significance in studies exploring the chemical origins of life and the prebiotic chemistry that may have led to the emergence of nucleic acids.

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>
MMDBc0057083

> <DATABASE_NAME>
MIME

> <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

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

Molecular Formula

C₉H₁₂N₃O₇P

Average Mass

305.1812

Monoisotopic Mass

305.041286265

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

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	22.3 g/L	ALOGPS
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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00kf-3910000000-7da8d8b4b4443ea9b3c4	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0901000000-2f9db91ff0f1874900d9	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-9af0c8dbbb12007337d8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-9600000000-609e9469201d9763d37b	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0w29-2968000000-1d3057af3f18f18a5b6d	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0400-9540000000-bbbf0bdd0bdb8f6a5a75	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-005c-9100000000-cdf2f85d695b64ed7814	2016-09-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novere N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasic I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttila M, Klipp E, Palsson BO, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492. [PubMed:18846089 ]

Showing metabocard for 3',5'-cyclic CMP (MMDBc0057083)

MOL for #<Metabolite:0x00007f8dc8facbe0>

3D MOL for #<Metabolite:0x00007f8dc8facbe0>

3D SDF for #<Metabolite:0x00007f8dc8facbe0>

3D-SDF for #<Metabolite:0x00007f8dc8facbe0>

PDB for #<Metabolite:0x00007f8dc8facbe0>

3D PDB for #<Metabolite:0x00007f8dc8facbe0>

SMILES for #<Metabolite:0x00007f8dc8facbe0>

INCHI for #<Metabolite:0x00007f8dc8facbe0>

Structure for #<Metabolite:0x00007f8dc8facbe0>

3D Structure for #<Metabolite:0x00007f8dc8facbe0>