Bovine Metabolome Database: Showing metabocard for dCTP (BMDB0000998)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (3) Show 3 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:39:41 UTC

Update Date

2020-05-21 16:29:00 UTC

BMDB ID

BMDB0000998

Secondary Accession Numbers

BMDB00998

Metabolite Identification

Common Name

dCTP

Description

dCTP, also known as deoxy-CTP, 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. dCTP is an extremely weak basic (essentially neutral) compound (based on its pKa). dCTP exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2'-Deoxycytidine 5'-triphosphate	ChEBI
Deoxycytidine 5'-triphosphate	ChEBI
Deoxycytidine triphosphate	ChEBI
2'-Deoxycytidine 5'-triphosphoric acid	Generator
Deoxycytidine 5'-triphosphoric acid	Generator
Deoxycytidine triphosphoric acid	Generator
2'-Deoxycytidine-5'-triphosphate	HMDB
Deoxy-CTP	HMDB
Deoxycytidine-triphosphate	HMDB
2'-Deoxycytidine 5'-triphosphate, 3H-labeled	HMDB
2'-Deoxycytidine 5'-triphosphate, p-(32)p-labeled	HMDB
2'-Deoxycytidine 5'-triphosphate, magnesium salt	HMDB
2'-Deoxycytidine 5'-triphosphate, p''-(32)p-labeled	HMDB
2'-DeoxyCTP	HMDB
2'-Deoxycytidine 5'-(tetrahydrogen triphosphate)	HMDB
2’-DeoxyCTP	HMDB
2’-Deoxycytidine 5’-(tetrahydrogen triphosphate)	HMDB
2’-Deoxycytidine 5’-triphosphate	HMDB
5'-DCTP	HMDB
5’-DCTP	HMDB
Deoxy-5'-CTP	HMDB
Deoxy-5’-CTP	HMDB
Deoxycytidine 5’-triphosphate	HMDB
dCTP	HMDB

Chemical Formula

C₉H₁₆N₃O₁₃P₃

Average Molecular Weight

467.1569

Monoisotopic Molecular Weight

466.989597149

IUPAC Name

({[({[(2R,3S,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

dCTP

CAS Registry Number

2056-98-6

SMILES

NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(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+/m0/s1

InChI Key

RGWHQCVHVJXOKC-SHYZEUOFSA-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
Hydroxypyrimidine
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Azacycle
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

2'-deoxycytidine phosphate (CHEBI:16311 )
pyrimidine 2'-deoxyribonucleoside 5'-triphosphate (CHEBI:16311 )
Deoxyribonucleotides (C00458 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm
Mitochondria
Nucleus

Physical Properties

State

Solid

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	-0.52	ALOGPS
logP	-3.3	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	0.99	ChemAxon
pKa (Strongest Basic)	0.21	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	35.21 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-03di-1900000000-3d90990d3831fc38abb6	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-03di-1900000000-3d90990d3831fc38abb6	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9734200000-676373c19e4530dc2572	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00dm-9207110000-47dd719accdfad2d1bb7	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 16V, negative	splash10-014i-0100900000-0c4be9d6bd044dcc30a0	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 21V, negative	splash10-066r-0703900000-fba71bd6110938a88717	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 28V, negative	splash10-0a4i-0903100000-bc9ee1b07578fee8fe60	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 34V, negative	splash10-0a4i-1912000000-502a328c4dd3b85b1261	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 41V, negative	splash10-0a4i-3910000000-24e79fde8d9f943e5918	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 47V, negative	splash10-0a6r-7910000000-97e0df7b280b0847ad0e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 56V, negative	splash10-056r-9600000000-76ddb7ea2b1e0425b8bf	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 64V, negative	splash10-004i-9300000000-d6ad5706c5825292a03c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 77V, negative	splash10-004i-9100000000-df323aba3fe0d34ef447	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 32V, negative	splash10-014i-0419100000-8e37a6184a56a1ce0b9e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 32V, negative	splash10-004i-9000000000-46d4cee1b5ac630ba9b8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 32V, negative	splash10-0a4i-0190000000-e5ee855f41773e79d603	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 32V, negative	splash10-0a4r-1950000000-00c42d75643af2669e6b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 32V, negative	splash10-014r-0119100000-ec7aadc4870ab3921ecc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 32V, negative	splash10-052r-0691000000-113e1278b4a989de2daa	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 32V, positive	splash10-0006-0900400000-65f4077bcb5020b2d9a1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 32V, positive	splash10-00di-0102900000-863c74032b703a479a57	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, positive	splash10-014i-0100900000-764a12da50ad51ce0497	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 12V, positive	splash10-03di-0900200000-7b013855e19e8393c74d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-939cbd147b029e517cc1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-2911000000-f4b496ca2bd6dcb38361	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-4900000000-a5e5fd690ddf51310279	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00xu-4110900000-42349a9362c5d3d7c6ef	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-057r-9540100000-7a06dee6889dcffec4e9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-056r-9610000000-0a85daf50b374c5ac8ba	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm
Mitochondria
Nucleus

Biospecimen Locations

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pyrimidine Metabolism		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000998

DrugBank ID

DB03258

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022359

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Deoxycytidine triphosphate

METLIN ID

5929

PubChem Compound

65091

PDB ID

Not Available

ChEBI ID

16311

References

Synthesis Reference

Hinz M; Gottschling D; Eritja R; Seliger H Synthesis and properties of 2'-deoxycytidine triphosphate carrying c-myc tag sequence. Nucleosides, nucleotides & nucleic acids (2000), 19(10-12), 1543-52.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Nucleoside diphosphate kinase 7

General function:: Nucleotide transport and metabolism
Specific function:: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
Gene Name:: NME7
Uniprot ID:: Q5E9Y9
Molecular weight:: 42599.0

Reactions

dCDP + Adenosine triphosphate → dCTP + ADP	details

Enzyme Details

2. dCTP pyrophosphatase 1

General function:: Involved in dCTP diphosphatase activity
Specific function:: Hydrolyzes deoxynucleoside triphosphates (dNTPs) to the corresponding nucleoside monophosphates. Has a strong preference for dCTP and its analogs including 5-iodo-dCTP and 5-methyl-dCTP for which it may even have a higher efficiency. May protect DNA or RNA against the incorporation of these genotoxic nucleotide analogs through their catabolism.
Gene Name:: DCTPP1
Uniprot ID:: Q32KY6
Molecular weight:: 18626.0

Enzyme Details

3. CTP synthase 2

General function:: Nucleotide transport and metabolism
Specific function:: Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Constitutes the rate-limiting enzyme in the synthesis of cytosine nucleotides (By similarity).
Gene Name:: CTPS2
Uniprot ID:: Q1RMS2
Molecular weight:: 65481.0

Reactions

Uridine triphosphate + Adenosine triphosphate → Cytidine triphosphate + ADP + Hydrogen phosphate + dCTP	details

Showing metabocard for dCTP (BMDB0000998)

Structure for BMDB0000998 (dCTP)

Enzymes

Reactions

Reactions