NP-MRD: Showing NP-Card for 3-methylcytidine (NP0168295)

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Record Information

Version

2.0

Created at

2022-09-03 04:04:16 UTC

Updated at

2022-09-03 04:04:16 UTC

NP-MRD ID

NP0168295

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-methylcytidine

Description

3-Methylcytidine belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. 5-Methylcytidine is a modified nucleoside derived from 5-methylcytosine. 3-methylcytidine is found in Geodia barretti. 3-Methylcytidine is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
   -4.6496    2.4596   -0.5050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4321    1.4844   -0.2563 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1974    1.0903   -0.0738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1383    1.9718   -0.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8766    1.4471    0.0067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6695    0.1673    0.3275 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6767   -0.2924    0.5336 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5950    0.7193    0.5905 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8136    0.2671    0.1694 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2891    1.0129   -1.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4192    2.3581   -0.8698 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6558   -1.1804   -0.2548 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8248   -2.0426    0.8333 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1653   -1.1495   -0.6150 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6106   -2.3999   -0.6362 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7087   -0.6657    0.4524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5703   -1.8823    0.7532 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9593   -0.1910    0.2496 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0866   -1.1201    0.3911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3209    2.9951   -0.4667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0290    2.1058   -0.0902 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7401   -0.9381    1.4465 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5997    0.3967    0.9404 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5536    0.8465   -1.9125 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2234    0.5446   -1.3985 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4345    2.6518    0.0570 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2728   -1.4521   -1.1104 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8969   -1.5139    1.6890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0199   -0.5938   -1.5392 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9855   -2.9816    0.0679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1406   -1.5470    1.3972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0260   -0.6001    0.1469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9716   -1.9678   -0.3309 H   0  0  0  0  0  0  0  0  0  0  0  0
 19 18  1  0
 18  3  1  0
  3  2  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
  6 16  1  0
 16 17  2  0
 16 18  1  0
 14  7  1  0
 19 31  1  0
 19 32  1  0
 19 33  1  0
  2  1  1  0
  4 20  1  0
  5 21  1  0
  7 22  1  1
  9 23  1  1
 10 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  6
 13 28  1  0
 14 29  1  6
 15 30  1  0
M  END


  Mrv1652310241917592D          

 18 19  0  0  0  0            999 V2000
 9999.908810001.5532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.696810001.5450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.1668 9999.6948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.880210000.1059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.687210000.9306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.119710000.1863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2589 9998.4567    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.687210000.1071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9727 9999.6946    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9727 9998.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6872 9998.4571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4017 9998.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4017 9999.6946    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10000.7859 9999.6119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.118510000.0969    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.373410000.8815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.198410000.8815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.453310000.0969    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 14 15  1  0  0  0  0
 14 18  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  8 13  1  0  0  0  0
 12 13  1  0  0  0  0
  8  5  2  0  0  0  0
  9  6  1  0  0  0  0
 10  7  2  0  0  0  0
 16  1  1  6  0  0  0
 15 13  1  1  0  0  0
 18  3  1  1  0  0  0
 17  2  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0168295

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N3O5/c1-12-6(11)2-3-13(10(12)17)9-8(16)7(15)5(4-14)18-9/h2-3,5,7-9,11,14-16H,4H2,1H3/t5-,7-,8-,9-/m1/s1

> <INCHI_KEY>
RDPUKVRQKWBSPK-ZOQUXTDFSA-N

> <FORMULA>
C10H15N3O5

> <MOLECULAR_WEIGHT>
257.246

> <EXACT_MASS>
257.101170595

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
24.42945309479645

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methyl-1,2,3,4-tetrahydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.71

> <JCHEM_LOGP>
-1.817037896

> <ALOGPS_LOGS>
-1.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.933965309537061

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.55383331073508

> <JCHEM_PKA_STRONGEST_BASIC>
-0.017893755025645386

> <JCHEM_POLAR_SURFACE_AREA>
117.31999999999998

> <JCHEM_REFRACTIVITY>
69.93430000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.43e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylcytidine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-OCT-19         0                                  
HETATM    1  O   UNK     0    8666.4968669.566   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8669.8348669.551   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8670.7118666.097   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8672.0438666.864   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8664.2168668.404   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0    8661.2908667.014   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0    8661.5508663.786   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0    8664.2168666.867   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0    8662.8828666.097   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0    8662.8828664.556   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8664.2168663.787   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8665.5508664.556   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0    8665.5508666.097   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0    8668.1348665.942   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0    8666.8888666.848   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8667.3648668.312   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8668.9048668.312   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8669.3798666.848   0.000  0.00  0.00           C+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3    4   18                                                       
CONECT    4    3                                                            
CONECT    5    8                                                            
CONECT    6    9                                                            
CONECT    7   10                                                            
CONECT    8    9   13    5                                                  
CONECT    9    8   10    6                                                  
CONECT   10   11    9    7                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13    8   12   15                                                  
CONECT   14   15   18                                                       
CONECT   15   16   14   13                                                  
CONECT   16   15   17    1                                                  
CONECT   17   16   18    2                                                  
CONECT   18   17   14    3                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
3-Methyl-4,N(4)-didehydro-3,4-dihydrocytidine	ChEBI
N3-Methylcytidine	HMDB
3-Methylcytidine	HMDB

Chemical Formula

C₁₀H₁₅N₃O₅

Average Mass

257.2460 Da

Monoisotopic Mass

257.10117 Da

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methyl-1,2,3,4-tetrahydropyrimidin-2-one

Traditional Name

3-methylcytidine

CAS Registry Number

Not Available

SMILES

CN1C(=N)C=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O

InChI Identifier

InChI=1S/C10H15N3O5/c1-12-6(11)2-3-13(10(12)17)9-8(16)7(15)5(4-14)18-9/h2-3,5,7-9,11,14-16H,4H2,1H3/t5-,7-,8-,9-/m1/s1

InChI Key

RDPUKVRQKWBSPK-ZOQUXTDFSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Geodia barretti	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Urea
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

methylcytidine (CHEBI:20129 )

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	-1.8	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-0.018	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	117.32 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	69.93 m³·mol⁻¹	ChemAxon
Polarizability	24.43 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

HMDB0240577

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

21864863

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

5-Methylcytidine

METLIN ID

Not Available

PubChem Compound

14237477

PDB ID

Not Available

ChEBI ID

20129

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-methylcytidine (NP0168295)

MOL for NP0168295 (3-methylcytidine)

3D MOL for NP0168295 (3-methylcytidine)

3D SDF for NP0168295 (3-methylcytidine)

3D-SDF for NP0168295 (3-methylcytidine)

PDB for NP0168295 (3-methylcytidine)

3D PDB for NP0168295 (3-methylcytidine)

SMILES for NP0168295 (3-methylcytidine)

INCHI for NP0168295 (3-methylcytidine)

Structure for NP0168295 (3-methylcytidine)

3D Structure for NP0168295 (3-methylcytidine)