Showing metabocard for 5-Methylcytosine (MMDBc0029700)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:38:05 UTC
Update Date2022-08-31 17:12:46 UTC
Metabolite IDMMDBc0029700
Metabolite Identification
Common Name5-Methylcytosine
Description5-Methylcytosine is a methylated form of cytosine in which a methyl group is attached to carbon 5, altering its structure without altering its base-pairing properties. 5-Methylcytosine is an epigenetic modification formed by the action of DNA methyltransferases. Its function varies significantly among species. In bacteria, 5-methylcytosine can be found at a variety of sites, and is often used as a marker to protect DNA from being cut by native methylation-sensitive restriction enzymes. (Wikipedia )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5a88f25ca8>


  Mrv0541 02231219362D          

  9  9  0  0  0  0            999 V2000
   27.7034  -16.9726    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.8455  -16.9726    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.2745  -16.9726    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.9890  -15.7350    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.8455  -15.3225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9890  -16.5601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5600  -16.5601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5600  -15.7350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.2745  -15.3225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  2  7  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  6  1  0  0  0  0
  4  9  2  0  0  0  0
  5  8  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f5a88f25ca8>

HMDB0002894
     RDKit          3D
5-Methylcytosine
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.0035    0.1811   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6211   -0.3092   -0.0881 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3304   -1.6501   -0.3019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9557   -2.0478   -0.2880 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9847   -1.2099   -0.0763 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1660   -1.6778   -0.0813 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7227    0.0927    0.1328 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4506    0.5326    0.1271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2111    1.9029    0.3493 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1978    0.9879    0.6204 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2616    0.5099   -1.1382 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7292   -0.6465    0.1629 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1594   -2.3264   -0.4727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5246    0.7450    0.2976 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6389    2.2902    0.8071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9266    2.6255    0.0415 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  8  2  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  7 14  1  0
  9 15  1  0
  9 16  1  0
M  END
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3D SDF for #<Metabolite:0x00007f5a88f25ca8>


  Mrv0541 02231219362D          

  9  9  0  0  0  0            999 V2000
   27.7034  -16.9726    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.8455  -16.9726    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.2745  -16.9726    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.9890  -15.7350    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.8455  -15.3225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9890  -16.5601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5600  -16.5601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5600  -15.7350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.2745  -15.3225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  2  7  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  6  1  0  0  0  0
  4  9  2  0  0  0  0
  5  8  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029700

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=C(N)NC(=O)N=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)

> <INCHI_KEY>
LRSASMSXMSNRBT-UHFFFAOYSA-N

> <FORMULA>
C5H7N3O

> <MOLECULAR_WEIGHT>
125.1286

> <EXACT_MASS>
125.058911861

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.885321543269935

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-5-methyl-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-0.63

> <JCHEM_LOGP>
-0.7520553023333332

> <ALOGPS_LOGS>
-1.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.078245303541685

> <JCHEM_PKA_STRONGEST_BASIC>
3.746117471149919

> <JCHEM_POLAR_SURFACE_AREA>
67.48

> <JCHEM_REFRACTIVITY>
42.371900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.91e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-methylcytosine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f5a88f25ca8>

HMDB0002894
     RDKit          3D
5-Methylcytosine
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.0035    0.1811   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6211   -0.3092   -0.0881 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3304   -1.6501   -0.3019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9557   -2.0478   -0.2880 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9847   -1.2099   -0.0763 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1660   -1.6778   -0.0813 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7227    0.0927    0.1328 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4506    0.5326    0.1271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2111    1.9029    0.3493 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1978    0.9879    0.6204 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2616    0.5099   -1.1382 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7292   -0.6465    0.1629 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1594   -2.3264   -0.4727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5246    0.7450    0.2976 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6389    2.2902    0.8071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9266    2.6255    0.0415 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  8  2  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  7 14  1  0
  9 15  1  0
  9 16  1  0
M  END
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PDB for #<Metabolite:0x00007f5a88f25ca8>

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  O   UNK     0      51.713 -31.682   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0      46.378 -31.682   0.000  0.00  0.00           N+0
HETATM    3  N   UNK     0      49.046 -31.682   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      50.379 -29.372   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      46.378 -28.602   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      50.379 -30.912   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      47.712 -30.912   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      47.712 -29.372   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      49.046 -28.602   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    7                                                            
CONECT    3    6    7                                                       
CONECT    4    6    9                                                       
CONECT    5    8                                                            
CONECT    6    1    3    4                                                  
CONECT    7    2    3    8                                                  
CONECT    8    5    7    9                                                  
CONECT    9    4    8                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for #<Metabolite:0x00007f5a88f25ca8>

COMPND    HMDB0002894
HETATM    1  C1  UNL     1       2.004   0.181  -0.092  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.621  -0.309  -0.088  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.330  -1.650  -0.302  1.00  0.00           C  
HETATM    4  N1  UNL     1      -0.956  -2.048  -0.288  1.00  0.00           N  
HETATM    5  C4  UNL     1      -1.985  -1.210  -0.076  1.00  0.00           C  
HETATM    6  O1  UNL     1      -3.166  -1.678  -0.081  1.00  0.00           O  
HETATM    7  N2  UNL     1      -1.723   0.093   0.133  1.00  0.00           N  
HETATM    8  C5  UNL     1      -0.451   0.533   0.127  1.00  0.00           C  
HETATM    9  N3  UNL     1      -0.211   1.903   0.349  1.00  0.00           N  
HETATM   10  H1  UNL     1       2.198   0.988   0.620  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.262   0.510  -1.138  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.729  -0.647   0.163  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.159  -2.326  -0.473  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.525   0.745   0.298  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.639   2.290   0.807  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.927   2.625   0.041  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    8    8
CONECT    3    4    4   13
CONECT    4    5
CONECT    5    6    6    7
CONECT    7    8   14
CONECT    8    9
CONECT    9   15   16
END
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SMILES for #<Metabolite:0x00007f5a88f25ca8>

CC1=C(N)NC(=O)N=C1
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INCHI for #<Metabolite:0x00007f5a88f25ca8>

InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)
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Synonyms
ValueSource
4-Amino-5-methyl-2(1H)-pyrimidinoneChEBI
4-Amino-5-methyl-2-pyrimidinolChEBI
4-Amino-5-methyl-2-(1H)-pyrimidinoneHMDB
5-Methyl-cytosineHMDB
5-Methylcytosine>96HMDB
Monohydrochloride, 5-methylcytosineHMDB
5 MethylcytosineHMDB
5 Methylcytosine monohydrochlorideHMDB
5-Methylcytosine monohydrochlorideHMDB
Molecular FormulaC5H7N3O
Average Mass125.1286
Monoisotopic Mass125.058911861
IUPAC Name6-amino-5-methyl-1,2-dihydropyrimidin-2-one
Traditional Name5-methylcytosine
CAS Registry Number554-01-8
SMILES
CC1=C(N)NC(=O)N=C1
InChI Identifier
InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)
InChI KeyLRSASMSXMSNRBT-UHFFFAOYSA-N