ECMDB: Xanthosine 5-triphosphate (ECMDB00293) (M2MDB000122)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (2)XML

Proteins (496)

Record Information

Version

2.0

Creation Date

2012-05-31 10:25:49 -0600

Update Date

2015-06-03 15:53:27 -0600

Secondary Accession Numbers

ECMDB00293

Identification

Name:

Xanthosine 5-triphosphate

Description

Xanthosine 5-triphosphate (XTP) is a Guanosine triphosphate (GTP) analogue. The base of XTP, xanthine, bears a keto group instead of an amino group at C2 of the purine rings. XTP can substitute for GTP in supporting receptor-mediated adenylyl cyclase activation. Xanthosine 5-triphosphate is an intermediate of the Purine metabolism pathway, a substrate of the enzymes dinucleoside tetraphosphatase (EC 3.6.1.17) and nucleoside-triphosphate pyrophosphatase (EC 3.6.1.19). It is also a substrate for Xanthine triphosphatase, which is a phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

5'-XTP
Xanthosine 5'-triphosphate
Xanthosine 5'-triphosphoric acid
Xanthosine 5-triphosphoric acid
Xanthosine mono(tetrahydrogen triphosphate)
Xanthosine mono(tetrahydrogen triphosphoric acid)
Xanthosine triphosphate
Xanthosine triphosphoric acid
XTP

Chemical Formula:

C₁₀H₁₅N₄O₁₅P₃

Weight:

Average: 524.1652
Monoisotopic: 523.974675366

InChI Key:

CAEFEWVYEZABLA-UUOKFMHZSA-N

InChI:

InChI=1S/C10H15N4O15P3/c15-5-3(1-26-31(22,23)29-32(24,25)28-30(19,20)21)27-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H2,12,13,17,18)/t3-,5-,6-,9-/m1/s1

CAS number:

6253-56-1

IUPAC Name:

({[({[(2R,3S,4R,5R)-5-(2,6-dihydroxy-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid

Traditional IUPAC Name:

xanthosine 5-triphosphate

SMILES:

O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O[C@H]([C@@H]1O)N1C=NC2=C1N=C(O)N=C2O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as purine ribonucleoside triphosphates. These are purine ribobucleotides with a triphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside triphosphates

Alternative Parents

Substituents

Purine ribonucleoside triphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Xanthine
Monosaccharide phosphate
Pentose monosaccharide
Imidazopyrimidine
Purine
Alkaloid or derivatives
Monoalkyl phosphate
Hydroxypyrimidine
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Tetrahydrofuran
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
1,2-diol
Organoheterocyclic compound
Azacycle
Oxacycle
Organopnictogen compound
Hydrocarbon derivative
Organic oxygen compound
Organic nitrogen compound
Alcohol
Organic oxide
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

xanthosine 5'-phosphate (CHEBI:10049 )
purine ribonucleoside 5'-triphosphate (CHEBI:10049 )

Physical Properties

State:

Solid

Charge:

-3

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	4.04 g/L	ALOGPS
logP	-0.45	ALOGPS
logP	-4.1	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	0.96	ChemAxon
pKa (Strongest Basic)	0.016	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	293.57 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	95.02 m³·mol⁻¹	ChemAxon
Polarizability	39.11 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

Water + Xanthosine 5-triphosphate > Hydrogen ion + Pyrophosphate + Xanthylic acid
Water + Xanthosine 5-triphosphate > Hydrogen ion + Phosphate + XDP
Guanosine triphosphate + Hydrogen ion + Water > Ammonium + Xanthosine 5-triphosphate
Xanthosine 5-triphosphate + Water <> Xanthylic acid + Pyrophosphate
Xanthosine 5-triphosphate + Water + 2'-Deoxyinosine triphosphate <> Xanthylic acid + Pyrophosphate + DIMP

SMPDB Pathways:

Collection of Reactions without pathways

PW001891

KEGG Pathways:

Purine metabolism ec00230
Thiamine metabolism ec00730

EcoCyc Pathways:

Not Available

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a6s-8956230000-c953b27fc23e558f8bc3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0fmi-3120921000-30ff3765201db0daec17	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 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 (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_16) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_17) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0911220000-7c9e13bd8e928a2e5785	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-840c07c15dbc79ad0f2e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-1900000000-bd6b424553d786306979	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0kor-1830690000-f39abfd999faa04d6195	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0kbf-9620000000-5b4fb80ecb79a0415518	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-056r-9710000000-ed7594e6df7e2139120b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900010000-34d38de7734016d84840	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-80965add49e2ab233b2c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0uxr-0982000000-f089c3e029edf74721dc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0000190000-79bde14d72b9665fa816	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9710120000-bccf656c48d8b7c059fa	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200100000-d64535400bb7e16803e7	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Klinker JF, Seifert R: Functionally nonequivalent interactions of guanosine 5'-triphosphate, inosine 5'-triphosphate, and xanthosine 5'-triphosphate with the retinal G-protein, transducin, and with Gi-proteins in HL-60 leukemia cell membranes. Biochem Pharmacol. 1997 Sep 1;54(5):551-62. Pubmed: 9337071
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195

Synthesis Reference:

anachkov I; Pan J Y; Wessling-Resnick M; Wright G E Synthesis and effect of nonhydrolyzable xanthosine triphosphate derivatives on prenylation of Rab5D136N. Molecular pharmacology (1997), 51(1), 47-51.

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	10049
HMDB ID	HMDB00293
Pubchem Compound ID	121887
Kegg ID	C00700
ChemSpider ID	388429
Wikipedia	XTP
BioCyc ID	XTP
EcoCyc ID	XTP

Enzymes

Protein Details

1. Nucleoside-triphosphatase rdgB

General function:: Involved in hydrolase activity
Specific function:: Hydrolyzes O6 atom-containing purine bases deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to nucleotide monophosphate and pyrophosphate. Probably excludes non- standard purines from DNA precursor pool, preventing thus incorporation into DNA and avoiding chromosomal lesions
Gene Name:: rdgB
Uniprot ID:: P52061
Molecular weight:: 21039

Reactions

A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate.

Protein Details

2. UPF0244 protein yjjX

General function:: Involved in nucleoside-triphosphatase activity
Specific function:: Specific function unknown
Gene Name:: yjjX
Uniprot ID:: P39411
Molecular weight:: 18213

Reactions

A nucleoside triphosphate + H(2)O = a nucleoside diphosphate + monophosphate.

Xanthosine 5-triphosphate (ECMDB00293) (M2MDB000122)

Structure for #<Compound:0x817b46d0>

Enzymes

Reactions

Reactions