MiMeDB: Showing metabocard for Deoxycytidine 5'-triphosphate (MMDBc0030388)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:06:23 UTC

Update Date

2022-08-31 17:50:27 UTC

Metabolite ID

MMDBc0030388

Metabolite Identification

Common Name

Deoxycytidine 5'-triphosphate

Description

Deoxycytidine triphosphate (dCTP) is a cytidine nucleotide triphosphate that is used whenever DNA is synthesized by DNA polymerase. During DNA synthesis dCTP has the PPi (pyrophosphate) cleaved off and the dCMP is incorporated into the DNA strand at the 3' end.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231216492D          

 28 29  0  0  1  0            999 V2000
   -1.3380   -0.4197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0025    0.3340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4874    1.0014    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1518    1.7551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6367    2.4225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3313    1.8413    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1536    1.1739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1820    0.4202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0042    2.5950    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4083    3.3094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1437    3.9225    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0278    4.7295    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8974    3.5870    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6119    3.9995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3264    3.5870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408    3.9995    0.0000 P   0  0  1  0  0  0  0  0  0  0  0  0
    3.4533    3.2850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6283    4.7140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7553    4.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4698    3.9995    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
    4.0573    3.2850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8823    4.7140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1842    3.5870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8987    3.9995    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.6132    4.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3112    3.2850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4862    4.7140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8112    2.7665    0.0000 O   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
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  9  6  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 16 15  1  1  0  0  0
 16 17  1  6  0  0  0
 16 18  2  0  0  0  0
 16 19  1  0  0  0  0
 20 19  1  6  0  0  0
 20 21  1  1  0  0  0
 20 22  2  0  0  0  0
 20 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 24 27  2  0  0  0  0
 13 28  1  0  0  0  0
  9 28  1  0  0  0  0
M  END


  Mrv0541 02231216492D          

 28 29  0  0  1  0            999 V2000
   -1.3380   -0.4197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0025    0.3340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4874    1.0014    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1518    1.7551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6367    2.4225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3313    1.8413    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1536    1.1739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1820    0.4202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0042    2.5950    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4083    3.3094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1437    3.9225    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0278    4.7295    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8974    3.5870    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6119    3.9995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3264    3.5870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408    3.9995    0.0000 P   0  0  1  0  0  0  0  0  0  0  0  0
    3.4533    3.2850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6283    4.7140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7553    4.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4698    3.9995    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
    4.0573    3.2850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8823    4.7140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1842    3.5870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8987    3.9995    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.6132    4.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3112    3.2850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4862    4.7140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8112    2.7665    0.0000 O   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
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  9  6  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 16 15  1  1  0  0  0
 16 17  1  6  0  0  0
 16 18  2  0  0  0  0
 16 19  1  0  0  0  0
 20 19  1  6  0  0  0
 20 21  1  1  0  0  0
 20 22  2  0  0  0  0
 20 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 24 27  2  0  0  0  0
 13 28  1  0  0  0  0
  9 28  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030388

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(=O)N(C=C1)[C@H]1C[C@@H](O)[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OP(O)(O)=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8-/m1/s1

> <INCHI_KEY>
RGWHQCVHVJXOKC-GKROBHDKSA-N

> <FORMULA>
C9H16N3O13P3

> <MOLECULAR_WEIGHT>
467.1569

> <EXACT_MASS>
466.989597149

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
35.292510539161356

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({[({[(2S,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
-0.52

> <JCHEM_LOGP>
-3.6348026734444794

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.5373176439976692

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.9467410634091911

> <JCHEM_PKA_STRONGEST_BASIC>
-0.05006454094108903

> <JCHEM_POLAR_SURFACE_AREA>
247.96999999999994

> <JCHEM_REFRACTIVITY>
85.6528

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.18e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
({[(2S,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxyphosphonic acid

> <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  N   UNK     0      -2.498  -0.783   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.871   0.623   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -2.776   1.869   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -2.150   3.276   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.055   4.522   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -0.618   3.437   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.287   2.191   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.340   0.784   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.008   4.844   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.762   6.178   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.268   7.322   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.052   8.828   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.675   6.696   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.009   7.466   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.343   6.696   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0       5.676   7.466   0.000  0.00  0.00           P+0
HETATM   17  O   UNK     0       6.446   6.132   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.906   8.799   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       7.010   8.236   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0       8.344   7.466   0.000  0.00  0.00           P+0
HETATM   21  O   UNK     0       7.574   6.132   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       9.114   8.799   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       9.677   6.696   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0      11.011   7.466   0.000  0.00  0.00           P+0
HETATM   25  O   UNK     0      12.345   8.236   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      11.781   6.132   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      10.241   8.799   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.514   5.164   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    2                                                       
CONECT    9    6   10   28                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   28                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16   20                                                       
CONECT   20   19   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20   24                                                       
CONECT   24   23   25   26   27                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   24                                                            
CONECT   28   13    9                                                       
MASTER        0    0    0    0    0    0    0    0   28    0   58    0
END

Synonyms

Value	Source
Deoxycytidine 5'-triphosphoric acid	Generator

Molecular Formula

C₉H₁₆N₃O₁₃P₃

Average Mass

467.1569

Monoisotopic Mass

466.989597149

IUPAC Name

({[({[(2S,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid

Traditional Name

({[(2S,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxyphosphonic acid

CAS Registry Number

2056-98-6

SMILES

NC1=NC(=O)N(C=C1)[C@H]1C[C@@H](O)[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OP(O)(O)=O)O1

InChI Identifier

InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8-/m1/s1

InChI Key

RGWHQCVHVJXOKC-GKROBHDKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside triphosphates. These are pyrimidine nucleotides with a triphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine deoxyribonucleotides

Direct Parent

Pyrimidine 2'-deoxyribonucleoside triphosphates

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	11.8 g/L	ALOGPS
logP	-0.52	ALOGPS
logP	-3.6	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	0.95	ChemAxon
pKa (Strongest Basic)	-0.05	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	247.97 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	85.65 m³·mol⁻¹	ChemAxon
Polarizability	35.29 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown

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

46936621

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, Goodacre R: Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal Chem. 2008 Apr 15;80(8):2939-48. doi: 10.1021/ac7023409. Epub 2008 Mar 11. [PubMed:18331064 ]

Showing metabocard for Deoxycytidine 5'-triphosphate (MMDBc0030388)

MOL for #<Metabolite:0x00007f124184b340>

3D MOL for #<Metabolite:0x00007f124184b340>

3D SDF for #<Metabolite:0x00007f124184b340>

3D-SDF for #<Metabolite:0x00007f124184b340>

PDB for #<Metabolite:0x00007f124184b340>

3D PDB for #<Metabolite:0x00007f124184b340>

SMILES for #<Metabolite:0x00007f124184b340>

INCHI for #<Metabolite:0x00007f124184b340>

Structure for #<Metabolite:0x00007f124184b340>

3D Structure for #<Metabolite:0x00007f124184b340>