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Showing metabocard for Xanthylic acid (HMDB0001554)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (14) Show 14 proteinsXML
enzymes (14) Show 14 proteins
Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-02-26 21:23:29 UTC
HMDB IDHMDB0001554
Secondary Accession Numbers
  • HMDB01554
Metabolite Identification
Common NameXanthylic acid
DescriptionXanthylic 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) Xanthylic acid can also be used in quantitative measurements of the Inosine monophosphate dehydrogenase enzyme activities in purine metabolism. This measurement is important for optimal thiopurine therapy for children with acute lymphoblastic leukaemia (ALL). (PMID: 16725387 ).
Structure
Data?1582752209
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(9-D-Ribosylxanthine)-5'-phosphateChEBI
Xanthosine 5'-phosphateChEBI
Xanthosine monophosphateChEBI
XMPChEBI
(9-D-Ribosylxanthine)-5'-phosphoric acidGenerator
Xanthosine 5'-phosphoric acidGenerator
Xanthosine monophosphoric acidGenerator
XanthylateGenerator
5'-Xanthonylate monophosphateHMDB
Xanthosine-5'-pHMDB
Xanthosine-5'-phosphateHMDB
Xanthosine monophosphate, 8-(14)C-labeledHMDB
Chemical FormulaC10H13N4O9P
Average Molecular Weight364.2054
Monoisotopic Molecular Weight364.042014546
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 Namexanthosine monophosphate
CAS Registry Number523-98-8
SMILES
O[C@@H]1[C@@H](COP(O)(O)=O)O[C@H]([C@@H]1O)N1C=NC2=C1NC(=O)NC2=O
InChI Identifier
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
InChI KeyDCTLYFZHFGENCW-UUOKFMHZSA-N
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct ParentPurine ribonucleoside monophosphates
Alternative Parents
Substituents
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Xanthine
  • 6-oxopurine
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Purinone
  • Imidazopyrimidine
  • Purine
  • Alkaloid or derivatives
  • Monoalkyl phosphate
  • Pyrimidone
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Pyrimidine
  • Heteroaromatic compound
  • Azole
  • Vinylogous amide
  • Imidazole
  • Tetrahydrofuran
  • Lactam
  • 1,2-diol
  • Urea
  • Secondary alcohol
  • Azacycle
  • Oxacycle
  • Organoheterocyclic compound
  • Alcohol
  • Organic oxide
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility2.49 g/LALOGPS
logP-2ALOGPS
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 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity73.08 m³·mol⁻¹ChemAxon
Polarizability29.99 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9613000000-3054f73e4c9456039ed6Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-01ot-9521200000-1e6fc3c628d8ebd23b37Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0ik9-7964000000-bce7ee60221f82790f35Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0002-9400000000-05c1ae772c001a15a8c6Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0913000000-d17f1d77b992fc6e9f04Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-efbdb918f50ba610575dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-2900000000-cf070bd16aacd3dcb6fbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0imi-6509000000-d931cb1dcaeba678220cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fbc-9300000000-e596281ec38113a9653cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-1caa46ecd17db343ddd3Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031254
KNApSAcK IDC00007396
Chemspider ID66054
KEGG Compound IDC00655
BioCyc IDNot Available
BiGG ID35623
Wikipedia LinkXanthosine monophosphate
METLIN IDNot Available
PubChem Compound73323
PDB IDNot Available
ChEBI ID15652
Food Biomarker OntologyNot Available
VMH IDXMP
References
Synthesis ReferenceHattori, Kyoji; Kawahara, Shin; Hagiwara, Takeshige. 5'-Xanthylic acid. Jpn. Kokai Tokkyo Koho (1985), 3 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. 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 ]
  6. 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 ]
  7. 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 ]
  8. 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 ]
  9. 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 ]
  10. 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 ]
  11. 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 ]
  12. 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 ]
  13. 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 ]
  14. 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 ]
  15. 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 ]
  16. 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 ]
  17. 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 ]
  18. 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 ]
  19. 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 ]
  20. 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 ]
  21. 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 ]
  22. 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 ]
  23. 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 ]
  24. Hedstrom L: IMP dehydrogenase: mechanism of action and inhibition. Curr Med Chem. 1999 Jul;6(7):545-60. [PubMed:10390600 ]

Only showing the first 10 proteins. There are 14 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. 5'-nucleotidase
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:
NT5E
Uniprot ID:
P21589
Molecular weight:
57948.125
Reactions
Xanthylic acid + Water → Xanthosine + Phosphatedetails
Enzyme Details
2. Cytosolic 5'-nucleotidase 1B
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Molecular weight:
68803.055
Reactions
Xanthylic acid + Water → Xanthosine + Phosphatedetails
Enzyme Details
3. Cytosolic 5'-nucleotidase 1A
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Molecular weight:
41020.145
Reactions
Xanthylic acid + Water → Xanthosine + Phosphatedetails
Enzyme Details
4. 5'(3')-deoxyribonucleotidase, cytosolic type
General function:
Involved in metal ion binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Molecular weight:
Not Available
Reactions
Xanthylic acid + Water → Xanthosine + Phosphatedetails
Enzyme Details
5. 5'(3')-deoxyribonucleotidase, mitochondrial
General function:
Involved in phosphatase activity
Specific function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Molecular weight:
Not Available
Reactions
Xanthylic acid + Water → Xanthosine + Phosphatedetails
Enzyme Details
6. Inosine triphosphate pyrophosphatase
General function:
Involved in hydrolase activity
Specific function:
Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) and xanthosine 5'-triphosphate (XTP) to their respective monophosphate derivatives. The enzyme does not distinguish between the deoxy- and ribose forms. Probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.
Gene Name:
ITPA
Uniprot ID:
Q9BY32
Molecular weight:
16833.23
Reactions
Xanthosine 5-triphosphate + Water → Xanthylic acid + Pyrophosphatedetails
Enzyme Details
7. Hypoxanthine-guanine phosphoribosyltransferase
General function:
Involved in hypoxanthine phosphoribosyltransferase activity
Specific function:
Converts guanine to guanosine monophosphate, and hypoxanthine to inosine monophosphate. Transfers the 5-phosphoribosyl group from 5-phosphoribosylpyrophosphate onto the purine. Plays a central role in the generation of purine nucleotides through the purine salvage pathway.
Gene Name:
HPRT1
Uniprot ID:
P00492
Molecular weight:
24579.155
Reactions
Xanthylic acid + Pyrophosphate → Xanthine + Phosphoribosyl pyrophosphatedetails
Enzyme Details
8. GMP synthase [glutamine-hydrolyzing]
General function:
Involved in catalytic activity
Specific function:
Involved in the de novo synthesis of guanine nucleotides which are not only essential for DNA and RNA synthesis, but also provide GTP, which is involved in a number of cellular processes important for cell division.
Gene Name:
GMPS
Uniprot ID:
P49915
Molecular weight:
76714.79
Reactions
Adenosine triphosphate + Xanthylic acid + L-Glutamine + Water → Adenosine monophosphate + Pyrophosphate + Guanosine monophosphate + L-Glutamic aciddetails
Adenosine triphosphate + Xanthylic acid + Ammonia → Adenosine monophosphate + Pyrophosphate + Guanosine monophosphatedetails
Enzyme Details
9. Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
General function:
Involved in hydrolase activity
Specific function:
Asymmetrically hydrolyzes Ap4A to yield AMP and ATP. Plays a major role in maintaining homeostasis.
Gene Name:
NUDT2
Uniprot ID:
P50583
Molecular weight:
16829.09
Reactions
P1,P4-Bis(5'-xanthosyl) tetraphosphate + Water → Xanthosine 5-triphosphate + Xanthylic aciddetails
Enzyme Details
10. Inosine-5'-monophosphate dehydrogenase 2
General function:
Involved in catalytic activity
Specific function:
Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism. It may also have a role in the development of malignancy and the growth progression of some tumors.
Gene Name:
IMPDH2
Uniprot ID:
P12268
Molecular weight:
55804.495
Reactions
Inosinic acid + NAD + Water → Xanthylic acid + NADHdetails
Inosinic acid + NAD + Water → Xanthylic acid + NADH + Hydrogen Iondetails

Only showing the first 10 proteins. There are 14 proteins in total.

Show all enzymes and transporters