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Showing metabocard for Cytosine (HMDB0000630)

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enzymes (3) Show 3 proteins
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
Data?1676999700
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
PropertyValueSource
Water Solubility30.9 g/LALOGPS
logP-0.94ALOGPS
logP-1.1ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)9.83ChemAxon
pKa (Strongest Basic)-0.06ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area67.48 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity38.01 m³·mol⁻¹ChemAxon
Polarizability9.88 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+120.57731661259
DarkChem[M-H]-115.42831661259
AllCCS[M+H]+123.87632859911
AllCCS[M-H]-118.00232859911
DeepCCS[M+H]+124.82630932474
DeepCCS[M-H]-122.54730932474
DeepCCS[M-2H]-158.730932474
DeepCCS[M+Na]+133.17530932474
AllCCS[M+H]+123.932859911
AllCCS[M+H-H2O]+118.932859911
AllCCS[M+NH4]+128.532859911
AllCCS[M+Na]+129.932859911
AllCCS[M-H]-118.032859911
AllCCS[M+Na-2H]-120.632859911
AllCCS[M+HCOO]-123.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CytosineNC1=CC=NC(=O)N12543.8Standard polar33892256
CytosineNC1=CC=NC(=O)N11407.7Standard non polar33892256
CytosineNC1=CC=NC(=O)N11526.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Cytosine,1TMS,isomer #1C[Si](C)(C)NC1=CC=NC(=O)[NH]11587.0Semi standard non polar33892256
Cytosine,1TMS,isomer #1C[Si](C)(C)NC1=CC=NC(=O)[NH]11613.2Standard non polar33892256
Cytosine,1TMS,isomer #1C[Si](C)(C)NC1=CC=NC(=O)[NH]12082.3Standard polar33892256
Cytosine,1TMS,isomer #2C[Si](C)(C)N1C(N)=CC=NC1=O1486.2Semi standard non polar33892256
Cytosine,1TMS,isomer #2C[Si](C)(C)N1C(N)=CC=NC1=O1528.3Standard non polar33892256
Cytosine,1TMS,isomer #2C[Si](C)(C)N1C(N)=CC=NC1=O2182.9Standard polar33892256
Cytosine,2TMS,isomer #1C[Si](C)(C)N(C1=CC=NC(=O)[NH]1)[Si](C)(C)C1465.9Semi standard non polar33892256
Cytosine,2TMS,isomer #1C[Si](C)(C)N(C1=CC=NC(=O)[NH]1)[Si](C)(C)C1640.2Standard non polar33892256
Cytosine,2TMS,isomer #1C[Si](C)(C)N(C1=CC=NC(=O)[NH]1)[Si](C)(C)C1937.1Standard polar33892256
Cytosine,2TMS,isomer #2C[Si](C)(C)NC1=CC=NC(=O)N1[Si](C)(C)C1630.6Semi standard non polar33892256
Cytosine,2TMS,isomer #2C[Si](C)(C)NC1=CC=NC(=O)N1[Si](C)(C)C1686.1Standard non polar33892256
Cytosine,2TMS,isomer #2C[Si](C)(C)NC1=CC=NC(=O)N1[Si](C)(C)C1890.2Standard polar33892256
Cytosine,3TMS,isomer #1C[Si](C)(C)N(C1=CC=NC(=O)N1[Si](C)(C)C)[Si](C)(C)C1665.1Semi standard non polar33892256
Cytosine,3TMS,isomer #1C[Si](C)(C)N(C1=CC=NC(=O)N1[Si](C)(C)C)[Si](C)(C)C1745.1Standard non polar33892256
Cytosine,3TMS,isomer #1C[Si](C)(C)N(C1=CC=NC(=O)N1[Si](C)(C)C)[Si](C)(C)C1741.5Standard polar33892256
Cytosine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1=CC=NC(=O)[NH]11816.5Semi standard non polar33892256
Cytosine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1=CC=NC(=O)[NH]11835.0Standard non polar33892256
Cytosine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1=CC=NC(=O)[NH]12245.7Standard polar33892256
Cytosine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C(N)=CC=NC1=O1704.5Semi standard non polar33892256
Cytosine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C(N)=CC=NC1=O1746.2Standard non polar33892256
Cytosine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C(N)=CC=NC1=O2257.7Standard polar33892256
Cytosine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=NC(=O)[NH]1)[Si](C)(C)C(C)(C)C1908.4Semi standard non polar33892256
Cytosine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=NC(=O)[NH]1)[Si](C)(C)C(C)(C)C2051.7Standard non polar33892256
Cytosine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=NC(=O)[NH]1)[Si](C)(C)C(C)(C)C2098.0Standard polar33892256
Cytosine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)NC1=CC=NC(=O)N1[Si](C)(C)C(C)(C)C2030.7Semi standard non polar33892256
Cytosine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)NC1=CC=NC(=O)N1[Si](C)(C)C(C)(C)C2101.7Standard non polar33892256
Cytosine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)NC1=CC=NC(=O)N1[Si](C)(C)C(C)(C)C2075.6Standard polar33892256
Cytosine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=NC(=O)N1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2252.3Semi standard non polar33892256
Cytosine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=NC(=O)N1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2351.3Standard non polar33892256
Cytosine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=NC(=O)N1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2081.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Cytosine GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0udm-3970000000-a0532c16ce61409499152014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Cytosine GC-MS (2 TMS)splash10-0udl-4790000000-f8d777863969fe9feeee2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Cytosine GC-MS (3 TMS)splash10-0h6s-2914000000-5c0c43de53d8e6d5ff652014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Cytosine GC-EI-TOF (Non-derivatized)splash10-0udm-3970000000-a0532c16ce61409499152017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Cytosine GC-MS (Non-derivatized)splash10-0udl-4790000000-f8d777863969fe9feeee2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Cytosine GC-MS (Non-derivatized)splash10-0h6s-2914000000-5c0c43de53d8e6d5ff652017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Cytosine GC-EI-TOF (Non-derivatized)splash10-0f6w-4960000000-b053578e0f2ae00d08082017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Cytosine GC-EI-TOF (Non-derivatized)splash10-0gxt-0914000000-bdca724db358d4bc5ccb2017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cytosine GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9400000000-109300546706ee372e622016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cytosine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-03di-1900000000-ce9c385be713873945a42012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-00kf-9100000000-5d27ff55f5080da7aaf02012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-0006-9100000000-585d7d52c8ceb70d1b252012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOFsplash10-03k9-0970000000-1491957a90e606f28d032012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOFsplash10-0006-9000000000-f79bcd2133156449152c2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOFsplash10-03di-0900000000-155769b79f7f2d14ee922012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOFsplash10-03di-0900000000-4b1d0c842bcd05ceed1b2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOFsplash10-03di-0910000000-7cd7c6a6f6e7c02ed6f12012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOFsplash10-0006-9000000000-71a5fe9af8fc82824d542012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOFsplash10-014i-0900000000-a210a634771936e0ffd62012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive-QTOFsplash10-03di-0900000000-084e35ced5f5834ca93e2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative-QTOFsplash10-03di-0900000000-d23ab5cfeba2d0a6ccff2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative-QTOFsplash10-02tc-9500000000-3b81b2a441135c25b1e32012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative-QTOFsplash10-00kf-9000000000-e57731b8ed024624cf7a2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative-QTOFsplash10-0006-9000000000-a1679050e95cc271b8b72012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative-QTOFsplash10-0006-9000000000-57b23eb60e1f7ce1ca972012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-QQ , negative-QTOFsplash10-03di-0900000000-d23ab5cfeba2d0a6ccff2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-QQ , negative-QTOFsplash10-02tc-9500000000-b9d5621a816bed354c102017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Cytosine LC-ESI-QQ , negative-QTOFsplash10-00kf-9000000000-e57731b8ed024624cf7a2017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cytosine 10V, Positive-QTOFsplash10-03di-1900000000-4047bc076c5529ab59532015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cytosine 20V, Positive-QTOFsplash10-03dj-9600000000-4b29d871234eed6b5e402015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cytosine 40V, Positive-QTOFsplash10-0uxv-9000000000-e7c1aa90d5d06c5c13b42015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cytosine 10V, Negative-QTOFsplash10-03di-2900000000-b19c12744f97185020072015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cytosine 20V, Negative-QTOFsplash10-014i-9100000000-1cf86d26f0f1d0794e0d2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cytosine 40V, Negative-QTOFsplash10-0006-9000000000-51460ed94e186a6f38e02015-05-27Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Quadrupole Ion Trap, ESI-, Adduct: [M-H]-)2022-02-11FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Quadrupole Ion Trap, ESI+, Adduct: [M+Na]+)2022-02-11FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Quadrupole Ion Trap, ESI+, Adduct: [M+H]+)2022-02-11FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
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
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
BloodDetected and Quantified6.4 +/- 8.5 uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Both
Normal		 details
UrineDetected and Quantified1.1-10.7 umol/mmol creatinineNewborn (0-30 days old)Both
Normal		 details
UrineDetected and Quantified4.1 (1.1-10.7) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.27 (0.21-0.42) umol/mmol creatinineNewborn (0-30 days old)Both
Normal
    • Analysis of 40 NI...
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)BothCrohns disease details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)BothUlcerative colitis details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedCrohns disease details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedUlcerative colitis details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedUnclassified IBD details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
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)Download (PDF)
General References
  1. Mills GC, Schmalstieg FC, Newkirk KE, Goldblum RM: Cytosine and orotic acid in urine of immunodeficient children. Clin Chem. 1979 Mar;25(3):419-24. [PubMed:262183 ]
  2. Rodriguez Ortner E, Hayes RB, Weissfeld J, Gelmann EP: Effect of homeodomain protein NKX3.1 R52C polymorphism on prostate gland size. Urology. 2006 Feb;67(2):311-5. Epub 2006 Jan 25. [PubMed:16442598 ]
  3. Harvey BG, Maroni J, O'Donoghue KA, Chu KW, Muscat JC, Pippo AL, Wright CE, Hollmann C, Wisnivesky JP, Kessler PD, Rasmussen HS, Rosengart TK, Crystal RG: Safety of local delivery of low- and intermediate-dose adenovirus gene transfer vectors to individuals with a spectrum of morbid conditions. Hum Gene Ther. 2002 Jan 1;13(1):15-63. [PubMed:11779412 ]
  4. Cheng JC, Yoo CB, Weisenberger DJ, Chuang J, Wozniak C, Liang G, Marquez VE, Greer S, Orntoft TF, Thykjaer T, Jones PA: Preferential response of cancer cells to zebularine. Cancer Cell. 2004 Aug;6(2):151-8. [PubMed:15324698 ]
  5. Carotti D, Funiciello S, Lavia P, Caiafa P, Strom R: Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase. Biochemistry. 1996 Sep 10;35(36):11660-7. [PubMed:8794746 ]
  6. Tawa R, Ueno S, Yamamoto K, Yamamoto Y, Sagisaka K, Katakura R, Kayama T, Yoshimoto T, Sakurai H, Ono T: Methylated cytosine level in human liver DNA does not decline in aging process. Mech Ageing Dev. 1992 Mar 1;62(3):255-61. [PubMed:1583911 ]
  7. Tsuchiya K, Tajima H, Yamada M, Takahashi H, Kuwae T, Sunaga K, Katsube N, Ishitani R: Disclosure of a pro-apoptotic glyceraldehyde-3-phosphate dehydrogenase promoter: anti-dementia drugs depress its activation in apoptosis. Life Sci. 2004 May 14;74(26):3245-58. [PubMed:15094325 ]
  8. Putta MR, Zhu F, Li Y, Bhagat L, Cong Y, Kandimalla ER, Agrawal S: Novel oligodeoxynucleotide agonists of TLR9 containing N3-Me-dC or N1-Me-dG modifications. Nucleic Acids Res. 2006 Jun 23;34(11):3231-8. Print 2006. [PubMed:16798912 ]
  9. Bawdon RE, Sobhi S, Dax J: The transfer of anti-human immunodeficiency virus nucleoside compounds by the term human placenta. Am J Obstet Gynecol. 1992 Dec;167(6):1570-4. [PubMed:1335207 ]
  10. Sawamura D, Abe R, Goto M, Akiyama M, Hemmi H, Akira S, Shimizu H: Direct injection of plasmid DNA into the skin induces dermatitis by activation of monocytes through toll-like receptor 9. J Gene Med. 2005 May;7(5):664-71. [PubMed:15655803 ]
  11. Thajeb P, Ma YS, Tzen CY, Chuang CK, Wu TY, Chen SC, Wei YH: Oculopharyngeal somatic myopathy in a patient with a novel large-scale 3,399 bp deletion and a homoplasmic T5814C transition of the mitochondrial DNA. Clin Neurol Neurosurg. 2006 Jun;108(4):407-10. [PubMed:16644408 ]
  12. Sigalotti L, Coral S, Nardi G, Spessotto A, Cortini E, Cattarossi I, Colizzi F, Altomonte M, Maio M: Promoter methylation controls the expression of MAGE2, 3 and 4 genes in human cutaneous melanoma. J Immunother. 2002 Jan-Feb;25(1):16-26. [PubMed:11924907 ]
  13. Costa E, Grayson DR, Mitchell CP, Tremolizzo L, Veldic M, Guidotti A: GABAergic cortical neuron chromatin as a putative target to treat schizophrenia vulnerability. Crit Rev Neurobiol. 2003;15(2):121-42. [PubMed:14977367 ]
  14. Machwe A, Orren DK, Bohr VA: Accelerated methylation of ribosomal RNA genes during the cellular senescence of Werner syndrome fibroblasts. FASEB J. 2000 Sep;14(12):1715-24. [PubMed:10973920 ]
  15. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

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