MiMeDB: Showing metabocard for N(4)-acetyl-2'-deoxycytidine (MMDBc0056182)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:18:54 UTC

Update Date

2025-10-07 16:09:37 UTC

Metabolite ID

MMDBc0056182

Metabolite Identification

Common Name

N(4)-acetyl-2'-deoxycytidine

Description

N(4)-acetyl-2'-deoxycytidine is a nucleoside derivative belonging to the class of modified deoxynucleosides. Its chemical structure features a deoxyribose sugar linked to a cytosine base that is acetylated at the N(4) position. This modification can influence the stability and reactivity of nucleic acids. N(4)-acetyl-2'-deoxycytidine is involved in various biochemical pathways, including the synthesis of CPD-containing oligonucleotides, where it plays a role in the formation of nucleic acid structures with specific properties. For instance, in a study focused on synthesizing these oligonucleotides, researchers prepared properly-protected thymidylyl-(3' 5')-N(4)-acetyl-2'-deoxycytidine and subjected it to UV irradiation using acetophenone as a sensitizer, highlighting its utility in photochemical applications (PMID:18776441 ). The acetyl group may also affect interactions with enzymes and other biomolecules, potentially influencing processes such as DNA replication and repair. Overall, N(4)-acetyl-2'-deoxycytidine serves as an important building block in the design of nucleic acid analogs and contributes to our understanding of nucleic acid chemistry.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222182D          

 22 23  0  0  1  0            999 V2000
    5.2527   -5.4220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9540   -2.5798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4691   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7678   -4.7546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  1  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
    4.6184   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3130   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1034   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7980   -3.4197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6486   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6860   -0.8436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9473   -4.8408    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
    2.4926   -2.8385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -1.1299    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7891   -2.0662    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  6  1  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  6  0  0  0
  8  7  1  0  0  0  0
  9  2  1  0  0  0  0
 10  4  1  0  0  0  0
 12  6  2  0  0  0  0
 12  9  1  4  0  0  0
 13  9  2  0  0  0  0
 13 11  1  0  0  0  0
 14  3  1  0  0  0  0
 10 14  1  6  0  0  0
 14 11  1  0  0  0  0
 15  5  1  0  0  0  0
 16  6  1  0  0  0  0
  7 17  1  1  0  0  0
 18 11  2  0  0  0  0
 19  8  1  0  0  0  0
 19 10  1  0  0  0  0
  7 20  1  6  0  0  0
  8 21  1  1  0  0  0
 10 22  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056182

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)C[C@@]([H])(O[C@]1([H])CO)N1C=CC(N=C(C)O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H15N3O5/c1-6(16)12-9-2-3-14(11(18)13-9)10-4-7(17)8(5-15)19-10/h2-3,7-8,10,15,17H,4-5H2,1H3,(H,12,13,16,18)/t7-,8+,10+/m0/s1

> <INCHI_KEY>
RWYFZABPLDFELM-QXFUBDJGSA-N

> <FORMULA>
C11H15N3O5

> <MOLECULAR_WEIGHT>
269.257

> <EXACT_MASS>
269.101170595

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
25.962371040627687

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-{1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxo-1,2-dihydropyrimidin-4-yl}ethanimidic acid

> <JCHEM_LOGP>
-1.5316367779999998

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.89494211918917

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.307270333504659

> <JCHEM_PKA_STRONGEST_BASIC>
0.7384070724451318

> <JCHEM_POLAR_SURFACE_AREA>
114.95

> <JCHEM_REFRACTIVITY>
62.9996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-{1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxopyrimidin-4-yl}ethanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       9.805 -10.121   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.247  -4.816   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.342  -3.570   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.425  -0.544   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.900  -8.875   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.621  -6.222   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.906  -2.485   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.184  -5.138   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       9.526  -7.468   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       7.090  -6.383   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       6.811  -3.731   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       1.281  -1.575   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.368  -9.036   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.653  -5.299   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       4.366  -2.485   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       3.763   0.584   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       2.801  -2.109   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       5.206  -3.857   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2    3    9                                                       
CONECT    3    2   14                                                       
CONECT    4    7   10                                                       
CONECT    5    8   15                                                       
CONECT    6    1   12   16                                                  
CONECT    7    4    8   17   20                                             
CONECT    8    5    7   19   21                                             
CONECT    9    2   12   13                                                  
CONECT   10    4   14   19   22                                             
CONECT   11   13   14   18                                                  
CONECT   12    6    9                                                       
CONECT   13    9   11                                                       
CONECT   14    3   10   11                                                  
CONECT   15    5                                                            
CONECT   16    6                                                            
CONECT   17    7                                                            
CONECT   18   11                                                            
CONECT   19    8   10                                                       
CONECT   20    7                                                            
CONECT   21    8                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₁₅N₃O₅

Average Mass

269.257

Monoisotopic Mass

269.101170595

IUPAC Name

N-{1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxo-1,2-dihydropyrimidin-4-yl}ethanimidic acid

Traditional Name

N-{1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxopyrimidin-4-yl}ethanimidic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)C[C@@]([H])(O[C@]1([H])CO)N1C=CC(N=C(C)O)=NC1=O

InChI Identifier

InChI=1S/C11H15N3O5/c1-6(16)12-9-2-3-14(11(18)13-9)10-4-7(17)8(5-15)19-10/h2-3,7-8,10,15,17H,4-5H2,1H3,(H,12,13,16,18)/t7-,8+,10+/m0/s1

InChI Key

RWYFZABPLDFELM-QXFUBDJGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
N-acetylarylamine
N-arylamide
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Oxolane
Heteroaromatic compound
Acetamide
Carboxamide group
Secondary alcohol
Secondary carboxylic acid amide
Carboxylic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary alcohol
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.5	ChemAxon
pKa (Strongest Acidic)	5.31	ChemAxon
pKa (Strongest Basic)	0.74	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	114.95 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	63 m³·mol⁻¹	ChemAxon
Polarizability	25.96 Å³	ChemAxon
Number of Rings	2	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 (TMS_2_3) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	200.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	114.1
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	124.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	279.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	266.2
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	216.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	926.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	212.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	373.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	155.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	214.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	154.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	83.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	159.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	416.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	62.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	196.1
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	886.4
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	598.5

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_1	CC(O)=NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C=C1	standard non polar	2025-10-24	1818.0
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_2	CC(O)=NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C)O2)C=C1	standard non polar	2025-10-24	2012.1
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_3	CC(=NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=C1)O[Si](C)(C)C	standard non polar	2025-10-24	1783.53
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_4	CC(=NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C=C1)O[Si](C)(C)C	standard non polar	2025-10-24	1323.59
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_5	CC(O)=NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=C1	standard non polar	2025-10-24	1920.24
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_6	CC(=NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C)O2)C=C1)O[Si](C)(C)C	standard non polar	2025-10-24	2246.34
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_7	CC(=NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=C1)O[Si](C)(C)C	standard non polar	2025-10-24	1822.92
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_1	CC(O)=NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C=C1	standard polar	2025-10-24	2812.7
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_2	CC(O)=NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C)O2)C=C1	standard polar	2025-10-24	2060.83
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_3	CC(=NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=C1)O[Si](C)(C)C	standard polar	2025-10-24	1947.25
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_4	CC(=NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C=C1)O[Si](C)(C)C	standard polar	2025-10-24	2509.03
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_5	CC(O)=NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=C1	standard polar	2025-10-24	2141.78
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_6	CC(=NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C)O2)C=C1)O[Si](C)(C)C	standard polar	2025-10-24	2112.13
Gas Chromatography	N(4)-acetyl-2'-deoxycytidine_TMS_7	CC(=NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=C1)O[Si](C)(C)C	standard polar	2025-10-24	2793.63

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/Eubacteria	Proteobacteria	75	Human ; Human feces; Chicken
Bacteria	Proteobacteria	5	Human ; Human feces; Chicken

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

9521166

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11346228

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 N(4)-acetyl-2'-deoxycytidine (MMDBc0056182)

MOL for #<Metabolite:0x00007f9aa4208488>

3D MOL for #<Metabolite:0x00007f9aa4208488>

3D SDF for #<Metabolite:0x00007f9aa4208488>

3D-SDF for #<Metabolite:0x00007f9aa4208488>

PDB for #<Metabolite:0x00007f9aa4208488>

3D PDB for #<Metabolite:0x00007f9aa4208488>

SMILES for #<Metabolite:0x00007f9aa4208488>

INCHI for #<Metabolite:0x00007f9aa4208488>

Structure for #<Metabolite:0x00007f9aa4208488>

3D Structure for #<Metabolite:0x00007f9aa4208488>