NP-MRD: Showing NP-Card for 5-Methyldeoxycytidine (NP0086915)

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Record Information

Version

2.0

Created at

2022-05-11 16:34:34 UTC

Updated at

2022-05-11 16:34:34 UTC

NP-MRD ID

NP0086915

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-Methyldeoxycytidine

Description

5-Methyldeoxycytidine, also known as 2'-deoxy-5-methylcytidine, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. 5-Methyldeoxycytidine is an extremely weak basic (essentially neutral) compound (based on its pKa). Levels of 5-mdc and the expression of nm23-H1 (an anti-metastatic gene identified in and human cancer lines) are highly correlated with human hepatoma cells with different invasion activities. 5-Methyldeoxycytidine was first documented in 2006 (PMID: 17044778). Methylation of cytosine-guanine dinucleotide sequences (CpG dinucleotides) catalyzed by DNA methyltransferase, particularly in the 5′-promoter regions of mammalian genes, forms 5-methyldeoxycytidine (5-mdc) whose levels may regulate gene expression (PMID: 17264127).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    3.4703    1.7498    0.5170 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7118    0.5153    0.1853 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3467    0.4339    0.3729 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6616   -0.6862    0.0715 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7306   -0.8617    0.2290 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3243   -0.0047    1.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7823   -0.3447    1.1042 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0284   -1.6492    1.4424 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7831   -0.2513   -0.4259 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2198    1.1877   -0.7331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5395    1.3161   -0.2677 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4998   -0.4902   -0.8414 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3923   -1.7131   -0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8016   -2.8036   -0.7271 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7065   -1.6641   -0.6129 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4319   -0.5613   -0.3242 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8387   -0.4937   -0.5235 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0051    1.6578    1.4938 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8107    2.6492    0.5193 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2563    1.9300   -0.2417 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7932    1.2571    0.7629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0096   -1.9151    0.5056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1982    1.0642    1.1632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9780   -0.3376    2.3420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4689    0.3848    1.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1147   -2.2613    0.6468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4978   -0.9691   -0.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1176    1.4308   -1.7967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6224    1.9109   -0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9576    0.4418   -0.3421 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3596    0.2036    0.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2867   -1.1261   -1.1962 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  4 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  5 22  1  1
  6 23  1  0
  6 24  1  0
  7 25  1  1
  8 26  1  0
  9 27  1  6
 10 28  1  0
 10 29  1  0
 11 30  1  0
 17 31  1  0
 17 32  1  0
M  END


  Mrv0541 02231219262D          

 17 18  0  0  1  0            999 V2000
   17.9364   -6.9742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3716   -8.4262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9868   -8.3401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8399   -5.6643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2690   -5.6643    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.5544   -4.4267    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.2690   -3.1893    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8564   -7.7589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2690   -6.4893    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.6014   -6.9742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6815   -7.7589    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.1662   -8.4262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9834   -5.2517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5544   -5.2517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9834   -4.4267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2690   -4.0143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6978   -4.0143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 11  1  0  0  0  0
  2  8  1  0  0  0  0
  3 12  1  0  0  0  0
  4 14  2  0  0  0  0
  9  5  1  6  0  0  0
  5 13  1  0  0  0  0
  5 14  1  0  0  0  0
  6 14  1  0  0  0  0
  6 16  2  0  0  0  0
  7 16  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
  9 10  1  0  0  0  0
 11 12  1  6  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086915

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N3O4/c1-5-3-13(10(16)12-9(5)11)8-2-6(15)7(4-14)17-8/h3,6-8,14-15H,2,4H2,1H3,(H2,11,12,16)/t6?,7-,8-/m1/s1

> <INCHI_KEY>
LUCHPKXVUGJYGU-SPDVFEMOSA-N

> <FORMULA>
C10H15N3O4

> <MOLECULAR_WEIGHT>
241.2438

> <EXACT_MASS>
241.106255983

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
23.341430172428066

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.71

> <JCHEM_LOGP>
-1.5013287319999995

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.787549172762255

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.894901399805956

> <JCHEM_PKA_STRONGEST_BASIC>
0.4056210110378124

> <JCHEM_POLAR_SURFACE_AREA>
108.37999999999998

> <JCHEM_REFRACTIVITY>
57.3912

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

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      33.481 -13.019   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.560 -15.729   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      35.442 -15.568   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      29.568 -10.573   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      32.235 -10.573   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      30.902  -8.263   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      32.235  -5.953   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      31.465 -14.483   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      32.235 -12.113   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      30.989 -13.019   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      33.005 -14.483   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      33.910 -15.729   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.569  -9.803   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      30.902  -9.803   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      33.569  -8.263   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      32.235  -7.493   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      34.903  -7.493   0.000  0.00  0.00           C+0
CONECT    1    9   11                                                       
CONECT    2    8                                                            
CONECT    3   12                                                            
CONECT    4   14                                                            
CONECT    5    9   13   14                                                  
CONECT    6   14   16                                                       
CONECT    7   16                                                            
CONECT    8    2   10   11                                                  
CONECT    9    1    5   10                                                  
CONECT   10    8    9                                                       
CONECT   11    1    8   12                                                  
CONECT   12    3   11                                                       
CONECT   13    5   15                                                       
CONECT   14    4    5    6                                                  
CONECT   15   13   16   17                                                  
CONECT   16    6    7   15                                                  
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Value	Source
2'-Deoxy-5-methylcytidine	HMDB
5-Methyl-2'-deoxycytidine	HMDB
5-Methyldeoxycytidine	MeSH

Chemical Formula

C₁₀H₁₅N₃O₄

Average Mass

241.2438 Da

Monoisotopic Mass

241.10626 Da

IUPAC Name

4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one

Traditional Name

4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one

CAS Registry Number

Not Available

SMILES

CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N

InChI Identifier

InChI=1S/C10H15N3O4/c1-5-3-13(10(16)12-9(5)11)8-2-6(15)7(4-14)17-8/h3,6-8,14-15H,2,4H2,1H3,(H2,11,12,16)/t6?,7-,8-/m1/s1

InChI Key

LUCHPKXVUGJYGU-SPDVFEMOSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.7	ALOGPS
logP	-1.5	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	0.41	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	57.39 m³·mol⁻¹	ChemAxon
Polarizability	23.34 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0002224

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022917

KNApSAcK ID

Not Available

Chemspider ID

12719

KEGG Compound ID

C03592

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13279

PDB ID

Not Available

ChEBI ID

27964

Good Scents ID

Not Available

References

General References

Yang TH, Hu ML: Intracellular levels of S-adenosylhomocysteine but not homocysteine are highly correlated to the expression of nm23-H1 and the level of 5-methyldeoxycytidine in human hepatoma cells with different invasion activities. Nutr Cancer. 2006;55(2):224-31. [PubMed:17044778 ]
Liu Z, Liu S, Xie Z, Blum W, Perrotti D, Paschka P, Klisovic R, Byrd J, Chan KK, Marcucci G: Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method. Nucleic Acids Res. 2007;35(5):e31. Epub 2007 Jan 30. [PubMed:17264127 ]

Showing NP-Card for 5-Methyldeoxycytidine (NP0086915)

MOL for NP0086915 (5-Methyldeoxycytidine)

3D MOL for NP0086915 (5-Methyldeoxycytidine)

3D SDF for NP0086915 (5-Methyldeoxycytidine)

3D-SDF for NP0086915 (5-Methyldeoxycytidine)

PDB for NP0086915 (5-Methyldeoxycytidine)

3D PDB for NP0086915 (5-Methyldeoxycytidine)

SMILES for NP0086915 (5-Methyldeoxycytidine)

INCHI for NP0086915 (5-Methyldeoxycytidine)

Structure for NP0086915 (5-Methyldeoxycytidine)

3D Structure for NP0086915 (5-Methyldeoxycytidine)