Showing metabocard for Cytosine (MMDBc0000126)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:36:49 UTC
Update Date2024-10-17 07:56:18 UTC
Metabolite IDMMDBc0000126
Metabolite Identification
Common NameCytosine
DescriptionCytosine is a pyrimidine base that is a fundamental unit of nucleic acids. The deamination of cytosine alone is apparent and the nucleotide of cytosine is the prime mutagenic nucleotide in leukaemia and cancer. Cytosine has been identified in the human placenta (PMID: 32033212 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fab032faf70>

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 #<Metabolite:0x00007fab032faf70>

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 #<Metabolite:0x00007fab032faf70>

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>
MMDBc0000126

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007fab032faf70>

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 #<Metabolite:0x00007fab032faf70>

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 #<Metabolite:0x00007fab032faf70>

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 #<Metabolite:0x00007fab032faf70>

NC1=CC=NC(=O)N1
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INCHI for #<Metabolite:0x00007fab032faf70>

InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
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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
Molecular FormulaC4H5N3O
Average Mass111.102
Monoisotopic Mass111.043261797
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