Xanthylic acid (PAMDB000419)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000419
Identification
Name: Xanthylic acid
Description:Xanthylic acid is an important metabolic intermediate in the purine metabolism, and is a product or substrate of the enzymes inosine monophosphate dehydrogenase (EC 1.1.1.205), hypoxanthine phosphoribosyltransferase (EC 2.4.2.8), xanthine phosphoribosyltransferase (EC 2.4.2.22), 5'-ribonucleotide phosphohydrolase (EC 3.1.3.5), Ap4A hydrolase (EC 3.6.1.17), nucleoside-triphosphate diphosphatase (EC 3.6.1.19), phosphoribosylamine-glycine ligase (EC 6.3.4.1), and glutamine amidotransferase (EC 6.3.5.2). (KEGG)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • (9-D-ribosylxanthine)-5'-phosphate
  • (9-D-Ribosylxanthine)-5'-phosphoric acid
  • 5'-Xanthonylate monophosphate
  • 5'-Xanthonylic acid monophosphate
  • 5'-Xanthonylic acid monophosphoric acid
  • 9-(5-phospho-β-D-ribosyl)xanthine
  • 9-(5-phospho-b-D-Ribosyl)xanthine
  • 9-(5-Phospho-beta-D-ribosyl)xanthine
  • 9-(5-phospho-β-D-Ribosyl)xanthine
  • Xanthosine 5'-phosphate
  • Xanthosine 5'-phosphoric acid
  • Xanthosine-5'-P
  • Xanthosine-5'-phosphate
  • Xanthosine-5'-phosphoric acid
  • Xanthosine-5-P
  • Xanthosine-5-phosphate
  • Xanthosine-5-phosphoric acid
  • Xanthylate
  • XMP
Chemical Formula: C10H13N4O9P
Average Molecular Weight: 364.2054
Monoisotopic Molecular Weight: 364.042014546
InChI Key: DCTLYFZHFGENCW-UUOKFMHZSA-N
InChI:InChI=1S/C10H13N4O9P/c15-5-3(1-22-24(19,20)21)23-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H2,19,20,21)(H2,12,13,17,18)/t3-,5-,6-,9-/m1/s1
CAS number: 523-98-8
IUPAC Name:{[(2R,3S,4R,5R)-5-(2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name: xanthosine monophosphate
SMILES:O[C@@H]1[C@@H](COP(O)(O)=O)O[C@H]([C@@H]1O)N1C=NC2=C1NC(=O)NC2=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as purine ribonucleoside monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Purine nucleotides
Sub ClassPurine ribonucleotides
Direct Parent Purine ribonucleoside monophosphates
Alternative Parents
Substituents
  • Purine ribonucleoside monophosphate
  • Alkaloid or derivatives
  • Xanthine
  • N-glycosyl compound
  • Glycosyl compound
  • Purinone
  • Monosaccharide phosphate
  • 6-oxopurine
  • Purine
  • Imidazopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Monosaccharide
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Imidazole
  • Azole
  • Urea
  • Secondary alcohol
  • Lactam
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility2.49 mg/mLALOGPS
logP-1.9ALOGPS
logP-2.2ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)1.26ChemAxon
pKa (Strongest Basic)0.069ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area192.47 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity73.08 m3·mol-1ChemAxon
Polarizability29.99 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Water + Xanthylic acid > Phosphate + Xanthosine
Phosphoribosyl pyrophosphate + Xanthine <> Pyrophosphate + Xanthylic acid
Adenosine triphosphate + L-Glutamine + Water + Xanthylic acid > Adenosine monophosphate + L-Glutamate + Guanosine monophosphate +2 Hydrogen ion + Pyrophosphate
Water + Inosinic acid + NAD <> Hydrogen ion + NADH + Xanthylic acid
Water + Xanthosine 5-triphosphate > Hydrogen ion + Pyrophosphate + Xanthylic acid
Adenosine triphosphate + Xanthylic acid + Ammonia <> Adenosine monophosphate + Pyrophosphate + Guanosine monophosphate
Adenosine triphosphate + Xanthylic acid + L-Glutamine + Water <> Adenosine monophosphate + Pyrophosphate + Guanosine monophosphate + L-Glutamate
Xanthosine 5-triphosphate + Water <> Xanthylic acid + Pyrophosphate
Adenosine triphosphate + Xanthylic acid + Ammonia > Hydrogen ion + Adenosine monophosphate + Pyrophosphate + Guanosine monophosphate
Inosinic acid + NAD + Water > Xanthylic acid + NADH
Xanthosine 5-triphosphate + Water + 2'-Deoxyinosine triphosphate <> Xanthylic acid + Pyrophosphate + DIMP
Adenosine triphosphate + Xanthylic acid + L-Glutamine + Water + Ammonia <> Adenosine monophosphate + Pyrophosphate + Guanosine monophosphate + L-Glutamate
Xanthylic acid + Adenosine triphosphate + L-Glutamine + Water > Adenosine monophosphate + Pyrophosphate + L-Glutamic acid +2 Hydrogen ion + Guanosine monophosphate + L-Glutamate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0913000000-d17f1d77b992fc6e9f04View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-efbdb918f50ba610575dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-2900000000-cf070bd16aacd3dcb6fbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0imi-6509000000-d931cb1dcaeba678220cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fbc-9300000000-e596281ec38113a9653cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-1caa46ecd17db343ddd3View in MoNA
References
References:
  • Albrecht W, Storck M, Pfetsch E, Martin W, Abendroth D: Development and application of a high-performance liquid chromatography-based assay for determination of the activity of inosine 5'-monophosphate dehydrogenase in whole blood and isolated mononuclear cells. Ther Drug Monit. 2000 Jun;22(3):283-94. Pubmed: 10850395
  • Barsotti C, Pesi R, Giannecchini M, Ipata PL: Evidence for the involvement of cytosolic 5'-nucleotidase (cN-II) in the synthesis of guanine nucleotides from xanthosine. J Biol Chem. 2005 Apr 8;280(14):13465-9. Epub 2005 Feb 6. Pubmed: 15699053
  • Daxecker H, Raab M, Muller MM: Influence of mycophenolic acid on inosine 5'-monophosphate dehydrogenase activity in human peripheral blood mononuclear cells. Clin Chim Acta. 2002 Apr;318(1-2):71-7. Pubmed: 11880114
  • Digits JA, Hedstrom L: Drug selectivity is determined by coupling across the NAD+ site of IMP dehydrogenase. Biochemistry. 2000 Feb 22;39(7):1771-7. Pubmed: 10677226
  • Digits JA, Hedstrom L: Species-specific inhibition of inosine 5'-monophosphate dehydrogenase by mycophenolic acid. Biochemistry. 1999 Nov 16;38(46):15388-97. Pubmed: 10563825
  • Franchetti P, Grifantini M: Nucleoside and non-nucleoside IMP dehydrogenase inhibitors as antitumor and antiviral agents. Curr Med Chem. 1999 Jul;6(7):599-614. Pubmed: 10390603
  • Frueh FW, Hayashibara KC, Brown PO, Whitlock JP Jr: Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expression. Toxicol Lett. 2001 Jul 6;122(3):189-203. Pubmed: 11489354
  • Glander P, Braun KP, Hambach P, Bauer S, Mai I, Roots I, Waiser J, Fritsche L, Neumayer HH, Budde K: Non-radioactive determination of inosine 5'-monophosphate dehydro-genase (IMPDH) in peripheral mononuclear cells. Clin Biochem. 2001 Oct;34(7):543-9. Pubmed: 11738390
  • Hedstrom L: IMP dehydrogenase: mechanism of action and inhibition. Curr Med Chem. 1999 Jul;6(7):545-60. Pubmed: 10390600
  • Heroux A, White EL, Ross LJ, Borhani DW: Crystal structures of the Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase-GMP and -IMP complexes: comparison of purine binding interactions with the XMP complex. Biochemistry. 1999 Nov 2;38(44):14485-94. Pubmed: 10545170
  • Heroux A, White EL, Ross LJ, Davis RL, Borhani DW: Crystal structure of Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase with XMP, pyrophosphate, and two Mg(2+) ions bound: insights into the catalytic mechanism. Biochemistry. 1999 Nov 2;38(44):14495-506. Pubmed: 10545171
  • Jayaram HN, Cooney DA, Grusch M, Krupitza G: Consequences of IMP dehydrogenase inhibition, and its relationship to cancer and apoptosis. Curr Med Chem. 1999 Jul;6(7):561-74. Pubmed: 10390601
  • 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
  • Khalil PN, Erb N, Khalil MN, Escherich G, Janka-Schaub GE: Validation and application of a high-performance liquid chromatographic-based assay for determination of the inosine 5'-monophosphate dehydrogenase activity in erythrocytes. J Chromatogr B Analyt Technol Biomed Life Sci. 2006 Sep 14;842(1):1-7. Epub 2006 May 24. Pubmed: 16725387
  • Markland W, McQuaid TJ, Jain J, Kwong AD: Broad-spectrum antiviral activity of the IMP dehydrogenase inhibitor VX-497: a comparison with ribavirin and demonstration of antiviral additivity with alpha interferon. Antimicrob Agents Chemother. 2000 Apr;44(4):859-66. Pubmed: 10722482
  • McMillan FM, Cahoon M, White A, Hedstrom L, Petsko GA, Ringe D: Crystal structure at 2.4 A resolution of Borrelia burgdorferi inosine 5'-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6. Biochemistry. 2000 Apr 18;39(15):4533-42. Pubmed: 10758003
  • Minakawa N, Matsuda A: Mechanism-based design of inosine 5-monophosphate dehydrogenase inhibitors: synthesis and biological activities of 5-ethynyl-1-beta-D-ribofuranosylimidazole-4-carboxamide (EICAR) and its derivatives. Curr Med Chem. 1999 Jul;6(7):615-28. Pubmed: 10390604
  • Pitera JW, Munagala NR, Wang CC, Kollman PA: Understanding substrate specificity in human and parasite phosphoribosyltransferases through calculation and experiment. Biochemistry. 1999 Aug 10;38(32):10298-306. Pubmed: 10441123
  • Prosise GL, Luecke H: Crystal structures of Tritrichomonasfoetus inosine monophosphate dehydrogenase in complex with substrate, cofactor and analogs: a structural basis for the random-in ordered-out kinetic mechanism. J Mol Biol. 2003 Feb 14;326(2):517-27. Pubmed: 12559919
  • Rauniyar RK, Suzuma K, King AL, Aiello LP, King GL: Differential effects of bactericidal/permeability-increasing protein (BPI) analogues on retinal neovascularization and retinal pericyte growth. Invest Ophthalmol Vis Sci. 2002 Feb;43(2):503-9. Pubmed: 11818397
  • Sintchak MD, Nimmesgern E: The structure of inosine 5'-monophosphate dehydrogenase and the design of novel inhibitors. Immunopharmacology. 2000 May;47(2-3):163-84. Pubmed: 10878288
  • Stoychev G, Kierdaszuk B, Shugar D: Xanthosine and xanthine. Substrate properties with purine nucleoside phosphorylases, and relevance to other enzyme systems. Eur J Biochem. 2002 Aug;269(16):4048-57. Pubmed: 12180982
  • 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
  • Vethe NT, Bergan S: Determination of inosine monophosphate dehydrogenase activity in human CD4+ cells isolated from whole blood during mycophenolic acid therapy. Ther Drug Monit. 2006 Oct;28(5):608-13. Pubmed: 17038874
  • Wall M, Shim JH, Benkovic SJ: Human AICAR transformylase: role of the 4-carboxamide of AICAR in binding and catalysis. Biochemistry. 2000 Sep 19;39(37):11303-11. Pubmed: 10985775
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
  • Wolan DW, Cheong CG, Greasley SE, Wilson IA: Structural insights into the human and avian IMP cyclohydrolase mechanism via crystal structures with the bound XMP inhibitor. Biochemistry. 2004 Feb 10;43(5):1171-83. Pubmed: 14756553
Synthesis Reference: Hattori, Kyoji; Kawahara, Shin; Hagiwara, Takeshige. 5'-Xanthylic acid. Jpn. Kokai Tokkyo Koho (1985), 3 pp.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID15652
HMDB IDHMDB01554
Pubchem Compound ID1190
Kegg IDC00655
ChemSpider ID66054
WikipediaXMP
BioCyc IDXANTHOSINE-5-PHOSPHATE
EcoCyc IDXANTHOSINE-5-PHOSPHATE
Ligand ExpoXMP

Enzymes

Protein Details
• GMP synthase [glutamine-hydrolyzing]
General function:
Involved in GMP synthase (glutamine-hydrolyzing) activity
Specific function:
Catalyzes the synthesis of GMP from XMP
Gene Name:
guaA
Locus Tag:
PA3769
Molecular weight:
58 kDa
Reactions
ATP + xanthosine 5'-phosphate + L-glutamine + H(2)O = AMP + diphosphate + GMP + L-glutamate.
Protein Details
• Multifunctional protein surE
General function:
Involved in hydrolase activity
Specific function:
Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of Pseudomonas aeruginosa in stationary growth phase
Gene Name:
surE
Locus Tag:
PA3625
Molecular weight:
26.4 kDa
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.
Protein Details
• Inosine-5'-monophosphate dehydrogenase
General function:
Involved in catalytic activity
Specific function:
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
Gene Name:
guaB
Locus Tag:
PA3770
Molecular weight:
51.7 kDa
Reactions
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH.
Protein Details
• Class B acid phosphatase
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Locus Tag:
PA1409
Molecular weight:
38 kDa
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.
Protein Details
• 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
Locus Tag:
PA0387
Molecular weight:
21.2 kDa
Reactions
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate.

Transporters