MiMeDB: Showing metabocard for 2',3'-Cyclic CMP (MMDBc0031552)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:38:54 UTC

Update Date

2022-08-31 18:21:42 UTC

Metabolite ID

MMDBc0031552

Metabolite Identification

Common Name

2',3'-Cyclic CMP

Description

2',3'-cyclic CMP is a member of the chemical class known as Pyrimidine 2'-deoxyribonucleosides and Analogues. These are compounds consisting of a pyrimidine linked to a ribose which lacks an hydroxyl group at position 2.

Structure

MOL SDF PDB SMILES InChI

 
  Mrv0541 07091216192D          
 
 20 22  0  0  1  0            999 V2000
   14.5928   -9.4217    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.8435   -8.6798    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.7753   -9.4217    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.8504  -10.1979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6301   -8.4222    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.1737   -8.1818    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5211   -8.6489    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.5246  -10.2014    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1875  -10.6823    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   16.2484   -8.9752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8019   -7.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7346   -8.3912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7679  -11.2628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5932  -11.2628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0384   -8.7142    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.0835   -9.7824    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5850   -7.3505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1197   -8.9409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2101   -7.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9967   -7.6459    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  1  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  6  0  0  0
  4  9  1  0  0  0  0
  5 10  1  0  0  0  0
  5 11  1  0  0  0  0
  7 12  1  1  0  0  0
  9 13  1  0  0  0  0
  9 14  2  0  0  0  0
 10 15  1  0  0  0  0
 10 16  2  0  0  0  0
 11 17  2  0  0  0  0
 12 18  1  0  0  0  0
 15 19  2  0  0  0  0
 19 20  1  0  0  0  0
  6  7  1  0  0  0  0
  8  9  1  0  0  0  0
 17 19  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031552

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@H]2OP(O)(=O)O[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N3O7P/c10-5-1-2-12(9(14)11-5)8-7-6(4(3-13)17-8)18-20(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>
NMPZCCZXCOMSDQ-XVFCMESISA-N

> <FORMULA>
C9H12N3O7P

> <MOLECULAR_WEIGHT>
305.1812

> <EXACT_MASS>
305.041286265

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
25.581594232724463

> <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]-4-amino-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.78

> <JCHEM_LOGP>
-2.2562422969105067

> <ALOGPS_LOGS>
-1.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.584903044550341

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.6486125153578648

> <JCHEM_PKA_STRONGEST_BASIC>
1.764223084638504

> <JCHEM_POLAR_SURFACE_AREA>
143.91

> <JCHEM_REFRACTIVITY>
61.63870000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JUL-12         0                                  
HETATM    1  C   UNK     0      27.240 -17.587   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      27.708 -16.202   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      25.714 -17.587   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      27.721 -19.036   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      29.176 -15.721   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      26.458 -15.273   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      25.239 -16.145   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      25.246 -19.043   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0      26.483 -19.940   0.000  0.00  0.00           P+0
HETATM   10  C   UNK     0      30.330 -16.754   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.497 -14.215   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      23.771 -15.664   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      27.567 -21.024   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      25.374 -21.024   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0      31.805 -16.266   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      30.022 -18.260   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      30.959 -13.721   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      22.623 -16.690   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      32.126 -14.747   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      33.594 -14.272   0.000  0.00  0.00           N+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10   11                                                  
CONECT    6    2    7                                                       
CONECT    7    3   12    6                                                  
CONECT    8    3    9                                                       
CONECT    9    4   13   14    8                                             
CONECT   10    5   15   16                                                  
CONECT   11    5   17                                                       
CONECT   12    7   18                                                       
CONECT   13    9                                                            
CONECT   14    9                                                            
CONECT   15   10   19                                                       
CONECT   16   10                                                            
CONECT   17   11   19                                                       
CONECT   18   12                                                            
CONECT   19   15   20   17                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Value	Source
CCMP	ChEBI
Cifostodina	ChEBI
Cifostodine	ChEBI
Cifostodinum	ChEBI
Citidine cyclic 2',3'-(hydrogen phosphate)	ChEBI
Citidine cyclic 2',3'-(hydrogen phosphoric acid)	Generator
Cifostodine barium (2:1) salt	MeSH
Cifostodine monosodium salt	MeSH
Cytidine 2',3'-phosphate	MeSH
Cytidine cyclic 2,3 monophosphate	MeSH
Cytidine cyclic-2',3'-monophosphate	MeSH

Molecular Formula

C₉H₁₂N₃O₇P

Average Mass

305.1812

Monoisotopic Mass

305.041286265

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]-4-amino-1,2-dihydropyrimidin-2-one

Traditional Name

2',3'-cyclic cmp

CAS Registry Number

633-90-9

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@H]2OP(O)(=O)O[C@@H]12

InChI Identifier

InChI=1S/C9H12N3O7P/c10-5-1-2-12(9(14)11-5)8-7-6(4(3-13)17-8)18-20(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

NMPZCCZXCOMSDQ-XVFCMESISA-N

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
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
1,3_dioxaphospholane
Organoheterocyclic compound
Oxacycle
Azacycle
Organic oxide
Primary alcohol
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic nitrogen compound
Primary amine
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

2',3'-cyclic pyrimidine nucleotide (CHEBI:27652 )
2',3'-Cyclic nucleotides (C02354 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	20.5 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.3	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	-0.65	ChemAxon
pKa (Strongest Basic)	1.76	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	2	ChemAxon
Refractivity	61.64 m³·mol⁻¹	ChemAxon
Polarizability	25.58 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

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
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	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

C02354

BioCyc ID

CPD-3713

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

68934

PDB ID

Not Available

ChEBI ID

27652

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for 2',3'-Cyclic CMP (MMDBc0031552)

MOL for #<Metabolite:0x00007f12408fdc08>

3D MOL for #<Metabolite:0x00007f12408fdc08>

3D SDF for #<Metabolite:0x00007f12408fdc08>

3D-SDF for #<Metabolite:0x00007f12408fdc08>

PDB for #<Metabolite:0x00007f12408fdc08>

3D PDB for #<Metabolite:0x00007f12408fdc08>

SMILES for #<Metabolite:0x00007f12408fdc08>

INCHI for #<Metabolite:0x00007f12408fdc08>

Structure for #<Metabolite:0x00007f12408fdc08>

3D Structure for #<Metabolite:0x00007f12408fdc08>