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Showing NP-Card for 5-Methylcytosine (NP0002733)

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Record Information
Version2.0
Created at2020-11-23 19:39:05 UTC
Updated at2024-09-03 04:16:49 UTC
NP-MRD IDNP0002733
Natural Product DOIhttps://doi.org/10.57994/0820
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-Methylcytosine
Provided ByBMRBBMRB logo
Description5-Methylcytosine belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 5-Methylcytosine exists in all living organisms, ranging from bacteria to humans. 5-Methylcytosine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 5-Methylcytosine is found in Luffa acutangula. 5-Methylcytosine was first documented in 2005 (PMID: 15748635). Based on a literature review very few articles have been published on 5-Methylcytosine (PMID: 17325422).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002733 (5-Methylcytosine)


     RDKit          2D

 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.0734    0.2942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5869    0.4944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0169    1.8819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4696    2.0821    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3863    0.8948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8729    1.0950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8164   -0.4927    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3298   -0.6929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2401   -2.0804    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2736    1.7808    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8733   -1.1923    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5600    0.0940    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9336    3.0693    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7330   -1.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765   -3.2677    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7267   -2.2806    0.0000 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  1
  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
Download

3D MOL for NP0002733 (5-Methylcytosine)

NP0002733
     RDKit          3D

 16 16  0  0  0  0  0  0  0  0999 V2000
   -1.8074   -0.7976   -0.2824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3500   -0.5951   -0.1555 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5785   -1.5873   -0.3332 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8970   -1.3131   -0.1974 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3515   -0.0839    0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5969    0.1183    0.2260 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4352    0.8864    0.2842 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1080    0.6674    0.1607 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8170    1.7265    0.3539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2298   -0.3524   -1.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3840   -0.3631    0.5657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0826   -1.8784   -0.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2113   -2.5723   -0.5804 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7622    1.8502    0.5243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4681    2.7026    0.2528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8018    1.5917    0.5856 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
Download

3D SDF for NP0002733 (5-Methylcytosine)


     RDKit          2D

 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.0734    0.2942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5869    0.4944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0169    1.8819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4696    2.0821    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3863    0.8948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8729    1.0950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8164   -0.4927    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3298   -0.6929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2401   -2.0804    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2736    1.7808    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8733   -1.1923    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5600    0.0940    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9336    3.0693    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7330   -1.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765   -3.2677    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7267   -2.2806    0.0000 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  1
  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
> <DATABASE_ID>
NP0002733

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0002733 (5-Methylcytosine)

NP0002733
     RDKit          3D

 16 16  0  0  0  0  0  0  0  0999 V2000
   -1.8074   -0.7976   -0.2824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3500   -0.5951   -0.1555 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5785   -1.5873   -0.3332 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8970   -1.3131   -0.1974 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3515   -0.0839    0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5969    0.1183    0.2260 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4352    0.8864    0.2842 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1080    0.6674    0.1607 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8170    1.7265    0.3539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2298   -0.3524   -1.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3840   -0.3631    0.5657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0826   -1.8784   -0.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2113   -2.5723   -0.5804 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7622    1.8502    0.5243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4681    2.7026    0.2528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8018    1.5917    0.5856 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
Download

PDB for NP0002733 (5-Methylcytosine)

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 NP0002733 (5-Methylcytosine)

COMPND    NP0002733
HETATM    1  C1  UNL     1      -1.807  -0.798  -0.282  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.350  -0.595  -0.156  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.578  -1.587  -0.333  1.00  0.00           C  
HETATM    4  N1  UNL     1       1.897  -1.313  -0.197  1.00  0.00           N  
HETATM    5  C4  UNL     1       2.352  -0.084   0.111  1.00  0.00           C  
HETATM    6  O1  UNL     1       3.597   0.118   0.226  1.00  0.00           O  
HETATM    7  N2  UNL     1       1.435   0.886   0.284  1.00  0.00           N  
HETATM    8  C5  UNL     1       0.108   0.667   0.161  1.00  0.00           C  
HETATM    9  N3  UNL     1      -0.817   1.727   0.354  1.00  0.00           N  
HETATM   10  H1  UNL     1      -2.230  -0.352  -1.206  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.384  -0.363   0.566  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.083  -1.878  -0.310  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.211  -2.572  -0.580  1.00  0.00           H  
HETATM   14  H5  UNL     1       1.762   1.850   0.524  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.468   2.703   0.253  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.802   1.592   0.586  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 NP0002733 (5-Methylcytosine)

CC1=C(N)NC(=O)N=C1
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INCHI for NP0002733 (5-Methylcytosine)

InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)
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View in JSmol
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-methylcytosineMeSH, HMDB
5 MethylcytosineMeSH, HMDB
5 Methylcytosine monohydrochlorideMeSH, HMDB
5-Methylcytosine monohydrochlorideMeSH, HMDB
Chemical FormulaC5H7N3O
Average Mass125.1286 Da
Monoisotopic Mass125.05891 Da
IUPAC Name6-amino-5-methyl-1,2-dihydropyrimidin-2-one
Traditional Name5-methylcytosine
CAS Registry NumberNot Available
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduNot AvailableNot Available2023-08-15View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)bgnzk@missouri.eduNot AvailableNot Available2023-08-15View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Luffa acutangulaLOTUS Database
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. 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 ParentHydroxypyrimidines
Alternative ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.63ALOGPS
logP-0.75ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)10.08ChemAxon
pKa (Strongest Basic)3.75ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area67.48 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.37 m³·mol⁻¹ChemAxon
Polarizability11.89 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002894
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB004432
KNApSAcK IDNot Available
Chemspider ID58551
KEGG Compound IDC02376
BioCyc IDCPD0-2018
BiGG IDNot Available
Wikipedia Link5-Methylcytosine
METLIN ID3247
PubChem Compound65040
PDB IDNot Available
ChEBI ID27551
Good Scents IDNot Available
References
General References
  1. Pfeifer GP, You YH, Besaratinia A: Mutations induced by ultraviolet light. Mutat Res. 2005 Apr 1;571(1-2):19-31. doi: 10.1016/j.mrfmmm.2004.06.057. Epub 2005 Jan 20. [PubMed:15748635 ]
  2. Widschwendter M: 5-methylcytosine--the fifth base of DNA: the fifth wheel on a car or a highly promising diagnostic and therapeutic target in cancer? Dis Markers. 2007;23(1-2):1-3. doi: 10.1155/2007/860404. [PubMed:17325422 ]