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Showing metabocard for Cytosine (HMDB0000630)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:55:51 UTC
HMDB IDHMDB0000630
Secondary Accession Numbers
  • HMDB00630
Metabolite Identification
Common NameCytosine
DescriptionCytosine, also known as C, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Cytosine is also classified as a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, cytosine forms three hydrogen bonds with guanine. Cytosine was discovered and named by Albrecht Kossel and Albert Neumann in 1894 when it was hydrolyzed from calf thymus tissues. Cytosine exists in all living species, ranging from bacteria to plants to humans. Within cells, cytosine can undergo several enzymatic reactions. It can be methylated into 5-methylcytosine by an enzyme called DNA methyltransferase (DNMT) or be methylated and hydroxylated to make 5-hydroxymethylcytosine. The DNA methyltransferase (DNMT) family of enzymes transfer a methyl group from S-adenosyl-l-methionine (SAM) to the 5’ carbon of cytosine in a molecule of DNA. High levels of cytosine can be found in the urine of individuals with severe combined immunodeficiency syndrome (SCID). Cytosine concentrations as high as (23-160 mmol/mol creatinine) were detected in SCID patients compared to normal levels of <2 mmol/mol creatinine (PMID: 262183 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000630 (Cytosine)

Cytosine.mol
  Mrv1652305271900072D          

  8  8  0  0  0  0            999 V2000
    0.7145    0.4125    0.0000 N   0  0  0  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
    1.4289   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 N   0  0  0  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
   -1.4289   -0.8250    0.0000 N   0  0  0  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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  1  8  2  0  0  0  0
M  END
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3D MOL for HMDB0000630 (Cytosine)

HMDB0000630
     RDKit          3D
Cytosine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.0368   -0.5045   -0.0051 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6575   -0.1295   -0.0033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2525    1.1775   -0.0764 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1043    1.4704   -0.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0191    0.4872    0.0071 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6169   -0.7910    0.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4942   -1.6999    0.1502 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2947   -1.0774    0.0722 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7741    0.1651    0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2946   -1.4684   -0.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0015    1.9600   -0.1381 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4585    2.4825   -0.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0293   -2.0721    0.1287 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  2  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  8 13  1  0
M  END
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3D SDF for HMDB0000630 (Cytosine)

Cytosine.mol
  Mrv1652305271900072D          

  8  8  0  0  0  0            999 V2000
    0.7145    0.4125    0.0000 N   0  0  0  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
    1.4289   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 N   0  0  0  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
   -1.4289   -0.8250    0.0000 N   0  0  0  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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  1  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000630

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=CC=NC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)

> <INCHI_KEY>
OPTASPLRGRRNAP-UHFFFAOYSA-N

> <FORMULA>
C4H5N3O

> <MOLECULAR_WEIGHT>
111.102

> <EXACT_MASS>
111.043261797

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.883975778125984

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-0.94

> <JCHEM_LOGP>
-1.1476057916666667

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.82715733969699

> <JCHEM_PKA_STRONGEST_BASIC>
-0.05985282344880383

> <JCHEM_POLAR_SURFACE_AREA>
67.48

> <JCHEM_REFRACTIVITY>
38.0148

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.09e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2(1H)-pyrimidinone, 6-amino-

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000630 (Cytosine)

HMDB0000630
     RDKit          3D
Cytosine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.0368   -0.5045   -0.0051 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6575   -0.1295   -0.0033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2525    1.1775   -0.0764 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1043    1.4704   -0.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0191    0.4872    0.0071 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6169   -0.7910    0.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4942   -1.6999    0.1502 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2947   -1.0774    0.0722 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7741    0.1651    0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2946   -1.4684   -0.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0015    1.9600   -0.1381 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4585    2.4825   -0.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0293   -2.0721    0.1287 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  2  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  8 13  1  0
M  END
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PDB for HMDB0000630 (Cytosine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Cytosine.mol                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0       1.334   0.770   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667  -1.540   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       0.000  -1.540   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -2.667  -1.540   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    8                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    1                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0000630 (Cytosine)

COMPND    HMDB0000630
HETATM    1  N1  UNL     1      -2.037  -0.505  -0.005  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.657  -0.130  -0.003  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.252   1.178  -0.076  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.104   1.470  -0.070  1.00  0.00           C  
HETATM    5  N2  UNL     1       2.019   0.487   0.007  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.617  -0.791   0.078  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.494  -1.700   0.150  1.00  0.00           O  
HETATM    8  N3  UNL     1       0.295  -1.077   0.072  1.00  0.00           N  
HETATM    9  H1  UNL     1      -2.774   0.165   0.230  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.295  -1.468  -0.248  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.001   1.960  -0.138  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.458   2.483  -0.126  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.029  -2.072   0.129  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3    3    8
CONECT    3    4   11
CONECT    4    5    5   12
CONECT    5    6
CONECT    6    7    7    8
CONECT    8   13
END
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SMILES for HMDB0000630 (Cytosine)

NC1=CC=NC(=O)N1
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INCHI for HMDB0000630 (Cytosine)

InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
4-Amino-2(1H)-pyrimidinoneChEBI
4-Amino-2-hydroxypyrimidineChEBI
CChEBI
CytChEBI
CytosinChEBI
ZytosinChEBI
4-Amino-2-oxo-1,2-dihydropyrimidineHMDB
4-AminouracilHMDB
CytosinimineHMDB
Chemical FormulaC4H5N3O
Average Molecular Weight111.102
Monoisotopic Molecular Weight111.043261797
IUPAC Name6-amino-1,2-dihydropyrimidin-2-one
Traditional Name2(1H)-pyrimidinone, 6-amino-
CAS Registry Number71-30-7
SMILES
NC1=CC=NC(=O)N1
InChI Identifier
InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
InChI KeyOPTASPLRGRRNAP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Aminopyrimidine
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility8 mg/mLNot Available
LogP-1.73HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Baker121.58330932474
[M+H]+Not Available121.583http://allccs.zhulab.cn/database/detail?ID=AllCCS00001960
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Blood
  • Epidermis
  • Fibroblasts
  • Intestine
  • Neuron
  • Placenta
  • Prostate
  • Skeletal Muscle
  • Spleen
  • Testis
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Crohn's disease
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Ulcerative colitis
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022151
KNApSAcK IDC00001498
Chemspider ID577
KEGG Compound IDC00380
BioCyc IDCYTOSINE
BiGG ID34812
Wikipedia LinkCytosine
METLIN ID283
PubChem Compound597
PDB IDNot Available
ChEBI ID16040
Food Biomarker OntologyNot Available
VMH IDCSN
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceHitchings, George H.; Elion, Gertrude B.; Falco, Elvira A.; Russell, Peter B. New synthesis of cytosine and 5-methylcytosine. Journal of Biological Chemistry (1949), 177 357-60.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Methyl-CpG-binding domain protein 2
General function:
Involved in DNA binding
Specific function:
Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemi-methylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. Isoform 1 may enhance the activation of some unmethylated cAMP-responsive promoters. Reports about DNA demethylase activity of isoform 2 are contradictory
Gene Name:
MBD2
Uniprot ID:
Q9UBB5
Molecular weight:
43254.3
Enzyme Details
2. APOBEC1 complementation factor
General function:
Involved in nucleotide binding
Specific function:
Essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. Binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. The complex also protects the edited APOB mRNA from nonsense-mediated decay
Gene Name:
A1CF
Uniprot ID:
Q9NQ94
Molecular weight:
65202.0
Enzyme Details
3. Methyl-CpG-binding domain protein 1
General function:
Involved in DNA binding
Specific function:
Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters
Gene Name:
MBD1
Uniprot ID:
Q9UIS9
Molecular weight:
66606.5