MiMeDB: Showing metabocard for Cytidine 2'-monophosphate (MMDBc0057137)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-11-09 19:12:20 UTC

Update Date

2024-10-13 07:22:48 UTC

Metabolite ID

MMDBc0057137

Metabolite Identification

Common Name

Cytidine 2'-monophosphate

Description

2'-cytidylic acid, also known as acid, cytidylic or 2' 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. 2'-cytidylic acid is a moderately basic compound (based on its pKa). A cytidine phosphate compound having the phosphate group at the 2'-position.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041401222D          

 25 26  0  0  1  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9346    0.6869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3206    0.3439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9561    1.3224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1276    0.5154    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612    0.2633    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3138    0.5418    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9547    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5238   -1.2021    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  1  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  2  0  0  0  0
 12  2  1  0  0  0  0
  8 12  1  1  0  0  0
 12  9  1  0  0  0  0
 13  3  1  0  0  0  0
  6 14  1  6  0  0  0
 15  9  1  0  0  0  0
 19  4  1  0  0  0  0
 19  8  1  0  0  0  0
  7 20  1  6  0  0  0
 21 16  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  2  0  0  0  0
 21 20  1  0  0  0  0
  4 22  1  6  0  0  0
  6 23  1  1  0  0  0
  7 24  1  1  0  0  0
  8 25  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057137

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(OP(O)(O)=O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(20-21(16,17)18)6(14)4(3-13)19-8/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
YQUAKORMLHPSLZ-XVFCMESISA-N

> <FORMULA>
C9H14N3O8P

> <MOLECULAR_WEIGHT>
323.1965

> <EXACT_MASS>
323.051850951

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
26.86220692741732

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.98

> <JCHEM_LOGP>
-3.2134018539694758

> <ALOGPS_LOGS>
-1.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.759030295360594

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.6476214809836227

> <JCHEM_PKA_STRONGEST_BASIC>
2.4313711557154547

> <JCHEM_POLAR_SURFACE_AREA>
176.13

> <JCHEM_REFRACTIVITY>
76.83019999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.46e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,4R,5R)-4-hydroxy-2-(2-hydroxy-4-iminopyrimidin-1-yl)-5-(hydroxymethyl)oxolan-3-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    5                                                       
CONECT    2    1   12                                                       
CONECT    3    4   13                                                       
CONECT    4    3    6   19   22                                             
CONECT    5    1   10   11                                                  
CONECT    6    4    7   14   23                                             
CONECT    7    6    8   20   24                                             
CONECT    8    7   12   19   25                                             
CONECT    9   11   12   15                                                  
CONECT   10    5                                                            
CONECT   11    5    9                                                       
CONECT   12    2    8    9                                                  
CONECT   13    3                                                            
CONECT   14    6                                                            
CONECT   15    9                                                            
CONECT   16   21                                                            
CONECT   17   21                                                            
CONECT   18   21                                                            
CONECT   19    4    8                                                       
CONECT   20    7   21                                                       
CONECT   21   16   17   18   20                                             
CONECT   22    4                                                            
CONECT   23    6                                                            
CONECT   24    7                                                            
CONECT   25    8                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

Synonyms

Value	Source
Cytidine 2'-monophosphate	ChEBI
Cytidine 2'-monophosphoric acid	Generator
2'-Cytidylate	Generator
monoPhosphate, cytidine	MeSH
Acid, cytidylic	MeSH
2' CMP	MeSH
3' CMP	MeSH
3'-CMP	MeSH
Acids, cytidylic	MeSH
2'-CMP	MeSH
Cytidylic acid	MeSH
Cytidine monophosphate	MeSH
CMP	MeSH
Cytidylic acids	MeSH
2'-Cytidylic acid	ChEBI
Cytidine 2'-phosphoric acid	Generator

Molecular Formula

C₉H₁₄N₃O₈P

Average Mass

323.1965

Monoisotopic Mass

323.051850951

IUPAC Name

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

Traditional Name

[(2R,3R,4R,5R)-4-hydroxy-2-(2-hydroxy-4-iminopyrimidin-1-yl)-5-(hydroxymethyl)oxolan-3-yl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(OP(O)(O)=O)[C@]1([H])O

InChI Identifier

InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(20-21(16,17)18)6(14)4(3-13)19-8/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChI Key

YQUAKORMLHPSLZ-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
Hydroxypyrimidine
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Primary alcohol
Alcohol
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

cytidine phosphate (CHEBI:28507 )
pyrimidine ribonucleoside 2'-monophosphate (CHEBI:28507 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	5.46 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3.2	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	0.65	ChemAxon
pKa (Strongest Basic)	2.43	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	176.13 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	76.83 m³·mol⁻¹	ChemAxon
Polarizability	26.86 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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	splash10-0002-9110000000-76c4763769592e6ae254	2017-08-28	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0911000000-2db366b9ffb4d361ebe1	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-5dddb811603cd00547d3	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3900000000-2bcac22a14bfa59c3b43	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-024i-7569000000-4b47c2bbbc6c399ff552	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9330000000-a3feb606b91bbabeba7e	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-f181f7e8ed56eef3a3b7	2017-07-26	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

Metabolic Reactions

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

Exposure Sources

Source Type	Activity	Data Source	Reference
Drugs	Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	Not Available	U.S. Environmental Protection Agency	CompTox
Domestics	Not Available	U.S. Environmental Protection Agency	CompTox

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

DB03765

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C03104

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101544

PDB ID

Not Available

ChEBI ID

28507

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Cytidine 2'-monophosphate (MMDBc0057137)

MOL for #<Metabolite:0x00007fdaff6ed750>

3D MOL for #<Metabolite:0x00007fdaff6ed750>

3D SDF for #<Metabolite:0x00007fdaff6ed750>

3D-SDF for #<Metabolite:0x00007fdaff6ed750>

PDB for #<Metabolite:0x00007fdaff6ed750>

3D PDB for #<Metabolite:0x00007fdaff6ed750>

SMILES for #<Metabolite:0x00007fdaff6ed750>

INCHI for #<Metabolite:0x00007fdaff6ed750>

Structure for #<Metabolite:0x00007fdaff6ed750>

3D Structure for #<Metabolite:0x00007fdaff6ed750>