Showing metabocard for N3-Methylcytosine (MMDBc0030205)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:58:17 UTC
Update Date2022-08-31 17:40:40 UTC
Metabolite IDMMDBc0030205
Metabolite Identification
Common NameN3-Methylcytosine
DescriptionN3-methylcytosine is a member of the chemical class known as Pyrimidones. These are compounds whose pyrimidine ring bears a ketone. 5-Methylcytosine is a methylated form of the DNA base cytosine that may be involved in the regulation of gene transcription. When cytosine is methylated, the DNA maintains the same sequence, but the expression of methylated genes can be altered (the study of this is part of the field of epigenetics). 5-Methylcytosine is incorporated in the nucleoside 5-methylcytidine. In 5-methylcytosine, a methyl group, is attached to the 5th carbon atom (counting counterclockwise from the NH nitrogen at the six o'clock position, not the 2 o'clock). This methyl group distinguishes 5-methylcytosine from cytosine. (WikiPedia)
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00005645c9dec7a8>


  Mrv0541 02231217252D          

  9  9  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -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
    0.0000    0.0000    0.0000 C   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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   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
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  CHG  1   2   1
M  END
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3D MOL for #<Metabolite:0x00005645c9dec7a8>

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3D SDF for #<Metabolite:0x00005645c9dec7a8>

  Mrv0541 02231217252D          

  9  9  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -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
    0.0000    0.0000    0.0000 C   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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   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
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  CHG  1   2   1
M  END
> <DATABASE_ID>
MMDBc0030205

> <DATABASE_NAME>
MIME

> <SMILES>
C[N+]1=C(N)C=CNC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H7N3O/c1-8-4(6)2-3-7-5(8)9/h2-3H,1H3,(H2,6,7,9)/p+1

> <INCHI_KEY>
UPHQQDZIRIHPHU-UHFFFAOYSA-O

> <FORMULA>
C5H8N3O

> <MOLECULAR_WEIGHT>
126.1365

> <EXACT_MASS>
126.066736893

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
12.268130171062573

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-1-methyl-2-oxo-2,3-dihydropyrimidin-1-ium

> <ALOGPS_LOGP>
-1.69

> <JCHEM_LOGP>
-4.301929061805079

> <ALOGPS_LOGS>
-1.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.520816361889803

> <JCHEM_PKA_STRONGEST_BASIC>
-4.820666774069685

> <JCHEM_POLAR_SURFACE_AREA>
58.13

> <JCHEM_REFRACTIVITY>
33.6452

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.15e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylcytosine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00005645c9dec7a8>
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PDB for #<Metabolite:0x00005645c9dec7a8>
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       4.001  -0.770   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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    2    9                                                  
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for #<Metabolite:0x00005645c9dec7a8>
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SMILES for #<Metabolite:0x00005645c9dec7a8>
C[N+]1=C(N)C=CNC1=O
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INCHI for #<Metabolite:0x00005645c9dec7a8>
InChI=1S/C5H7N3O/c1-8-4(6)2-3-7-5(8)9/h2-3H,1H3,(H2,6,7,9)/p+1
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SynonymsNot Available
Molecular FormulaC5H8N3O
Average Mass126.1365
Monoisotopic Mass126.066736893
IUPAC Name6-amino-1-methyl-2-oxo-2,3-dihydropyrimidin-1-ium
Traditional Name3-methylcytosine
CAS Registry NumberNot Available
SMILES
C[N+]1=C(N)C=CNC1=O
InChI Identifier
InChI=1S/C5H7N3O/c1-8-4(6)2-3-7-5(8)9/h2-3H,1H3,(H2,6,7,9)/p+1
InChI KeyUPHQQDZIRIHPHU-UHFFFAOYSA-O