MiMeDB: Showing metabocard for 5-methyl-CTP (MMDBc0055574)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:59:13 UTC

Update Date

2025-10-07 16:09:12 UTC

Metabolite ID

MMDBc0055574

Metabolite Identification

Common Name

5-methyl-CTP

Description

5-methyl-CTP is a modified nucleotide belonging to the class of nucleoside triphosphates. Its chemical structure features a cytidine base with a methyl group attached at the 5-position of the pyrimidine ring, which distinguishes it from canonical cytidine triphosphate (CTP). This modification can influence the stability and functionality of nucleic acids during various biochemical processes. 5-methyl-CTP is involved in several biochemical pathways, including its role as a substrate for DNA polymerases, as evidenced by studies investigating its incorporation into DNA strands during polymerization reactions (PMID:19300826 ). Additionally, it has been shown to participate in nucleotide pyrophosphatase activity, where prokaryotic and eukaryotic Maf proteins act on 5-methyl-CTP alongside other modified nucleotides and canonical nucleotides (PMID:24210219 ). Furthermore, 5-methyl-CTP has been utilized in innovative methods for partial restriction digestion of DNA fragments, showcasing its utility in molecular biology techniques (PMID:9321677 ). Overall, 5-methyl-CTP serves as an important component in various nucleic acid-related processes, contributing to the complexity of cellular metabolism and genetic regulation.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221592D          

 34 35  0  0  1  0            999 V2000
   -4.3455   -0.1418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0401    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5251   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1895   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6744   -1.6491    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3690   -1.0679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0636   -0.4867    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.1076    1.4239    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.5779    0.3843    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0680    1.9535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7825    0.9785    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2726    2.5477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3732    0.8529    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4773    2.0791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7429    1.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5384    0.9140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3122    2.0180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3230    1.1689    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.5275    1.7631    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.9253    1.4660    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5257    2.6201    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0573    2.6647    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5730    1.2219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3602    0.2856    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  1  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  9  7  1  0  0  0  0
 11  8  2  0  0  0  0
 12  8  1  0  0  0  0
 12 10  2  0  0  0  0
 13  2  1  0  0  0  0
  9 13  1  1  0  0  0
 13 10  1  0  0  0  0
  6 14  1  6  0  0  0
  7 15  1  6  0  0  0
 16 10  1  0  0  0  0
 24  3  1  0  0  0  0
 25  5  1  0  0  0  0
 25  9  1  0  0  0  0
 28 17  1  0  0  0  0
 28 18  1  0  0  0  0
 28 19  2  0  0  0  0
 28 26  1  0  0  0  0
 29 20  1  0  0  0  0
 29 21  2  0  0  0  0
 29 24  1  0  0  0  0
 29 27  1  0  0  0  0
 30 22  1  0  0  0  0
 30 23  2  0  0  0  0
 30 26  1  0  0  0  0
 30 27  1  0  0  0  0
  5 31  1  6  0  0  0
  6 32  1  1  0  0  0
  7 33  1  1  0  0  0
  9 34  1  6  0  0  0
M  CHG  4  16  -1  17  -1  18  -1  20  -1
M  END


  Mrv1652306172221592D          

 34 35  0  0  1  0            999 V2000
   -4.3455   -0.1418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0401    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5251   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1895   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6744   -1.6491    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3690   -1.0679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0636   -0.4867    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.1076    1.4239    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.5779    0.3843    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0680    1.9535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7825    0.9785    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2726    2.5477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3732    0.8529    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4773    2.0791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7429    1.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5384    0.9140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3122    2.0180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3230    1.1689    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.5275    1.7631    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.9253    1.4660    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5257    2.6201    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0573    2.6647    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5730    1.2219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3602    0.2856    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  1  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  9  7  1  0  0  0  0
 11  8  2  0  0  0  0
 12  8  1  0  0  0  0
 12 10  2  0  0  0  0
 13  2  1  0  0  0  0
  9 13  1  1  0  0  0
 13 10  1  0  0  0  0
  6 14  1  6  0  0  0
  7 15  1  6  0  0  0
 16 10  1  0  0  0  0
 24  3  1  0  0  0  0
 25  5  1  0  0  0  0
 25  9  1  0  0  0  0
 28 17  1  0  0  0  0
 28 18  1  0  0  0  0
 28 19  2  0  0  0  0
 28 26  1  0  0  0  0
 29 20  1  0  0  0  0
 29 21  2  0  0  0  0
 29 24  1  0  0  0  0
 29 27  1  0  0  0  0
 30 22  1  0  0  0  0
 30 23  2  0  0  0  0
 30 26  1  0  0  0  0
 30 27  1  0  0  0  0
  5 31  1  6  0  0  0
  6 32  1  1  0  0  0
  7 33  1  1  0  0  0
  9 34  1  6  0  0  0
M  CHG  4  16  -1  17  -1  18  -1  20  -1
M  END
> <DATABASE_ID>
MMDBc0055574

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)[C@@]([H])(O)[C@@]([H])(O[C@]1([H])COP([O-])(=O)OP(O)(=O)OP([O-])([O-])=O)N1C=C(C)C(=N)N=C1[O-]

> <INCHI_IDENTIFIER>
InChI=1S/C10H18N3O14P3/c1-4-2-13(10(16)12-8(4)11)9-7(15)6(14)5(25-9)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h2,5-7,9,14-15H,3H2,1H3,(H,20,21)(H,22,23)(H2,11,12,16)(H2,17,18,19)/p-4/t5-,6-,7-,9-/m1/s1

> <INCHI_KEY>
YIJVOACVHQZMKI-JXOAFFINSA-J

> <FORMULA>
C10H14N3O14P3

> <MOLECULAR_WEIGHT>
493.152

> <EXACT_MASS>
492.971057456

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
36.899094319516

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy(phosphonooxy)phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-4-imino-5-methyl-1,4-dihydropyrimidin-2-olate

> <JCHEM_LOGP>
-3.829454381593511

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.7383449752737357

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8835193223691329

> <JCHEM_PKA_STRONGEST_BASIC>
2.203246726418125

> <JCHEM_POLAR_SURFACE_AREA>
280.51

> <JCHEM_REFRACTIVITY>
110.11829999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy(phosphonooxy)phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-4-imino-5-methylpyrimidin-2-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -8.112  -0.265   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.675   0.820   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.242   3.846   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.580  -0.426   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.714   3.370   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.954  -1.832   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.238   1.905   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.517  -0.748   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -6.859  -3.078   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -4.422  -1.993   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      -4.143   0.659   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      -2.468   5.815   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -5.179   3.846   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.985  -0.909   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0       9.534   2.658   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       8.545   0.717   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0       7.594   3.647   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       3.327   1.826   0.000  0.00  0.00           O-1
HETATM   21  O   UNK     0       2.376   4.756   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.430   1.592   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.491   3.881   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.387   2.815   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -1.698   1.905   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       6.605   1.706   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       4.316   3.767   0.000  0.00  0.00           O+0
HETATM   28  P   UNK     0       8.070   2.182   0.000  0.00  0.00           P+0
HETATM   29  P   UNK     0       2.851   3.291   0.000  0.00  0.00           P+0
HETATM   30  P   UNK     0       5.460   2.737   0.000  0.00  0.00           P+0
HETATM   31  H   UNK     0      -0.981   4.891   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0      -3.840   4.974   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0      -4.803   2.281   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0      -2.539   0.533   0.000  0.00  0.00           H+0
CONECT    1    4                                                            
CONECT    2    4   13                                                       
CONECT    3    5   24                                                       
CONECT    4    1    2    8                                                  
CONECT    5    3    6   25   31                                             
CONECT    6    5    7   14   32                                             
CONECT    7    6    9   15   33                                             
CONECT    8    4   11   12                                                  
CONECT    9    7   13   25   34                                             
CONECT   10   12   13   16                                                  
CONECT   11    8                                                            
CONECT   12    8   10                                                       
CONECT   13    2    9   10                                                  
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16   10                                                            
CONECT   17   28                                                            
CONECT   18   28                                                            
CONECT   19   28                                                            
CONECT   20   29                                                            
CONECT   21   29                                                            
CONECT   22   30                                                            
CONECT   23   30                                                            
CONECT   24    3   29                                                       
CONECT   25    5    9                                                       
CONECT   26   28   30                                                       
CONECT   27   29   30                                                       
CONECT   28   17   18   19   26                                             
CONECT   29   20   21   24   27                                             
CONECT   30   22   23   26   27                                             
CONECT   31    5                                                            
CONECT   32    6                                                            
CONECT   33    7                                                            
CONECT   34    9                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   70    0
END

Synonyms

Not Available

Molecular Formula

C₁₀H₁₄N₃O₁₄P₃

Average Mass

493.152

Monoisotopic Mass

492.971057456

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy(phosphonooxy)phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-4-imino-5-methyl-1,4-dihydropyrimidin-2-olate

Traditional Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy(phosphonooxy)phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-4-imino-5-methylpyrimidin-2-olate

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)[C@@]([H])(O)[C@@]([H])(O[C@]1([H])COP([O-])(=O)OP(O)(=O)OP([O-])([O-])=O)N1C=C(C)C(=N)N=C1[O-]

InChI Identifier

InChI=1S/C10H18N3O14P3/c1-4-2-13(10(16)12-8(4)11)9-7(15)6(14)5(25-9)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h2,5-7,9,14-15H,3H2,1H3,(H,20,21)(H,22,23)(H2,11,12,16)(H2,17,18,19)/p-4/t5-,6-,7-,9-/m1/s1

InChI Key

YIJVOACVHQZMKI-JXOAFFINSA-J

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Alcohol
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.8	ChemAxon
pKa (Strongest Acidic)	0.88	ChemAxon
pKa (Strongest Basic)	2.2	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	280.51 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	110.12 m³·mol⁻¹	ChemAxon
Polarizability	36.9 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	511.2
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	271.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	128.1
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	427.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	313.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	213.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	831.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	192.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	675.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	144.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	252.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	157.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	57.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	533.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	402.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	54.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	197.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1008.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	636.2

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	5-methyl-CTP_TMS_1	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O)C([O-])=NC1=N	standard non polar	2025-10-24	1921.87
Gas Chromatography	5-methyl-CTP_TMS_2	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N	standard non polar	2025-10-24	2509.45
Gas Chromatography	5-methyl-CTP_TMS_3	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O)C([O-])=NC1=N	standard non polar	2025-10-24	293.201
Gas Chromatography	5-methyl-CTP_TMS_4	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O)C([O-])=NC1=N[Si](C)(C)C	standard non polar	2025-10-24	2745.62
Gas Chromatography	5-methyl-CTP_TMS_5	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N	standard non polar	2025-10-24	1048.67
Gas Chromatography	5-methyl-CTP_TMS_6	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O)C([O-])=NC1=N	standard non polar	2025-10-24	1274.43
Gas Chromatography	5-methyl-CTP_TMS_7	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O)C([O-])=NC1=N[Si](C)(C)C	standard non polar	2025-10-24	1909.33
Gas Chromatography	5-methyl-CTP_TMS_8	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N	standard non polar	2025-10-24	2040.69
Gas Chromatography	5-methyl-CTP_TMS_9	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N[Si](C)(C)C	standard non polar	2025-10-24	2875.75
Gas Chromatography	5-methyl-CTP_TMS_10	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O)C([O-])=NC1=N[Si](C)(C)C	standard non polar	2025-10-24	106.241
Gas Chromatography	5-methyl-CTP_TMS_11	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N	standard non polar	2025-10-24	1203.99
Gas Chromatography	5-methyl-CTP_TMS_12	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N[Si](C)(C)C	standard non polar	2025-10-24	2839.51
Gas Chromatography	5-methyl-CTP_TMS_13	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O)C([O-])=NC1=N[Si](C)(C)C	standard non polar	2025-10-24	1590.26
Gas Chromatography	5-methyl-CTP_TMS_14	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N[Si](C)(C)C	standard non polar	2025-10-24	2848.46
Gas Chromatography	5-methyl-CTP_TMS_15	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N[Si](C)(C)C	standard non polar	2025-10-24	1946.23
Gas Chromatography	5-methyl-CTP_TMS_1	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O)C([O-])=NC1=N	standard polar	2025-10-24	2006.9
Gas Chromatography	5-methyl-CTP_TMS_2	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N	standard polar	2025-10-24	2387.33
Gas Chromatography	5-methyl-CTP_TMS_3	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O)C([O-])=NC1=N	standard polar	2025-10-24	1831.24
Gas Chromatography	5-methyl-CTP_TMS_4	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O)C([O-])=NC1=N[Si](C)(C)C	standard polar	2025-10-24	1849.42
Gas Chromatography	5-methyl-CTP_TMS_5	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N	standard polar	2025-10-24	449.648
Gas Chromatography	5-methyl-CTP_TMS_6	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O)C([O-])=NC1=N	standard polar	2025-10-24	2829.3
Gas Chromatography	5-methyl-CTP_TMS_7	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O)C([O-])=NC1=N[Si](C)(C)C	standard polar	2025-10-24	1554.93
Gas Chromatography	5-methyl-CTP_TMS_8	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N	standard polar	2025-10-24	2519.84
Gas Chromatography	5-methyl-CTP_TMS_9	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N[Si](C)(C)C	standard polar	2025-10-24	1879.92
Gas Chromatography	5-methyl-CTP_TMS_10	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O)C([O-])=NC1=N[Si](C)(C)C	standard polar	2025-10-24	2989.71
Gas Chromatography	5-methyl-CTP_TMS_11	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N	standard polar	2025-10-24	1534.43
Gas Chromatography	5-methyl-CTP_TMS_12	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N[Si](C)(C)C	standard polar	2025-10-24	1591.47
Gas Chromatography	5-methyl-CTP_TMS_13	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O)C([O-])=NC1=N[Si](C)(C)C	standard polar	2025-10-24	1228.02
Gas Chromatography	5-methyl-CTP_TMS_14	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N[Si](C)(C)C	standard polar	2025-10-24	2415.01
Gas Chromatography	5-methyl-CTP_TMS_15	CC1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C([O-])=NC1=N[Si](C)(C)C	standard polar	2025-10-24	2759.32

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	1	Human feces
Bacteria	Proteobacteria	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

135563706

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 5-methyl-CTP (MMDBc0055574)

MOL for #<Metabolite:0x00007f9ab6f32e30>

3D MOL for #<Metabolite:0x00007f9ab6f32e30>

3D SDF for #<Metabolite:0x00007f9ab6f32e30>

3D-SDF for #<Metabolite:0x00007f9ab6f32e30>

PDB for #<Metabolite:0x00007f9ab6f32e30>

3D PDB for #<Metabolite:0x00007f9ab6f32e30>

SMILES for #<Metabolite:0x00007f9ab6f32e30>

INCHI for #<Metabolite:0x00007f9ab6f32e30>

Structure for #<Metabolite:0x00007f9ab6f32e30>

3D Structure for #<Metabolite:0x00007f9ab6f32e30>